Differential analysis (polarity)

Runs differential analysis on polarity scores generated with the Pixelator data processing pipeline.

Usage

RunDPA(object, ...)

# S3 method for class 'data.frame'
RunDPA(
  object,
  contrast_column,
  reference,
  targets = NULL,
  group_vars = NULL,
  polarity_metric = "morans_z",
  min_n_obs = 0,
  cl = NULL,
  alternative = c("two.sided", "less", "greater"),
  conf_int = TRUE,
  p_adjust_method = c("bonferroni", "holm", "hochberg", "hommel", "BH", "BY", "fdr"),
  verbose = TRUE,
  ...
)

# S3 method for class 'Seurat'
RunDPA(
  object,
  contrast_column,
  reference,
  targets = NULL,
  assay = NULL,
  group_vars = NULL,
  polarity_metric = "morans_z",
  min_n_obs = 0,
  cl = NULL,
  alternative = c("two.sided", "less", "greater"),
  conf_int = TRUE,
  p_adjust_method = c("bonferroni", "holm", "hochberg", "hommel", "BH", "BY", "fdr"),
  verbose = TRUE,
  ...
)

Arguments

object: An object containing polarity scores
...: Not yet implemented
contrast_column: The name of the column where the group labels are stored. This column must include target and reference.
reference: The name of the reference group
targets: The names of the target groups. These groups will be compared to the reference group. If the value is set to NULL (default), all groups available in contrast_column except reference will be compared to the reference group.
group_vars: An optional character vector with column names to group the tests by.
polarity_metric: The polarity metric to use. Any numeric data column in the polarity score table can be selected. The default is "morans_z".
min_n_obs: Minimum number of observations allowed in a group. Target groups with less observations than min_n_obs will be skipped.
cl: A cluster object created by makeCluster, or an integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations. See Details on performance in the documentation for pbapply. The default is NULL, which means that no parallelization is used. Note that warnings are not caught when using parallel processing.
alternative: One of 'two.sided', 'less' or 'greater' (see ?wilcox.test for details)
conf_int: Should confidence intervals be computed? (see ?wilcox.test for details)
p_adjust_method: One of "bonferroni", "holm", "hochberg", "hommel", "BH", "BY" or "fdr". (see ?p.adjust for details)
verbose: Print messages
assay: Name of assay to use

Value

A tbl_df object with test results

Details

If you are working with a Seurat object created with pixelatorR that contains a CellGraphAssay, the polarity scores are accessed directly from the CellGraphAssay (see PolarizationScores).

The input object should contain a contrast_column (character vector or factor) that includes information about the groups to compare. A typical example is a column with sample labels, for instance: "control", "stimulated1", "stimulated2". If the input object is a Seurat object, the contrast_column should be available in the meta.data slot. For those familiar with FindMarkers from Seurat, contrast_column is equivalent to the group.by parameter.

The targets parameter specifies a character vector with the names of the groups to compare reference. targets can be a single group name or a vector of group names while reference can only refer to a single group. Both targets and reference should be present in the contrast_column. These parameters are similar to the ident.1 and ident.2 parameters in FindMarkers.

Additional groups

The test is always computed between targets and reference, but it is possible to add additional grouping variables with group_vars. If group_vars is used, each comparison is split into groups defined by the group_vars. For instance, if we have annotated cells into cell type populations and saved these annotations in a meta.data column called "cell_type", we can pass "cell_type" to group_vars="cell_type" to split tests across each cell type.

Types of comparisons

Consider a scenario where we have a Seurat object (seurat_object) with MPX data. seurat_object contains a meta.data column called "sampleID" that holds information about what samples the MPX components originated from. This column could have three sample IDs: "control", "stimulated1" and "stimulated2". In addition, we have a column called "cell_type" that holds information about the cell type identity of each MPX component.

If we want to compare the "stimulated1" group to the "control" group:


dpa_markers <- RunDPA(object = seurat_object,
                      contrast_column = "sampleID",
                      reference = "control",
                      targets = "stimulated1")

If we want to compare the "stimulated1" and "stimulated2" groups to the "control" group:


dpa_markers <- RunDPA(object = seurat_object,
                      contrast_column = "sampleID",
                      reference = "control",
                      targets = c("stimulated1", "stimulated2"))

If we want to compare the "stimulated1" and "stimulated2" groups to the "control" group, and split the tests by cell type:


dpa_markers <- RunDPA(object = seurat_object,
                     contrast_column = "sampleID",
                     reference = "control",
                     targets = c("stimulated1", "stimulated2"),
                     group_vars = "cell_type")

Error handling

If the test fails for a certain comparison, a warning is raised and no results will be returned for that comparison. This can happen if one of the two groups being compared has too few observations. Note that when using parallel processing, these warnings are muted to reduce the overhead of communication between processes.

Examples

library(pixelatorR)
library(dplyr)

pxl_file <- system.file("extdata/five_cells",
  "five_cells.pxl",
  package = "pixelatorR"
)

# Load polarization scores
polarization_table1 <- polarization_table2 <- ReadMPX_polarization(pxl_file)
#> ℹ Loading item(s) from: /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/Rtmpn9YTAb/temp_libpath1398336799173/pixelatorR/extdata/five_cells/five_cells.pxl
#> →   Loading polarization data
#> ✔ Returning a 'tbl_df' object
polarization_table1$sample <- "Sample1"
polarization_table2$sample <- "Sample2"
polarization_table_merged <- bind_rows(polarization_table1, polarization_table2)

# Run DPA using table as input
dpa_markers <- RunDPA(polarization_table_merged,
  contrast_column = "sample",
  targets = "Sample1", reference = "Sample2"
)
#> ℹ Splitting data by: marker
#> ℹ Polarity metric: 'morans_z'
#> ℹ Running 80 tests for the following comparison:
#>   - Sample1 vs Sample2
#> Warning: Got the following message when running wilcox.test test for marker 'ACTB': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'B2M': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD102': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD11a': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD11b': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD11c': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD127': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD137': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD14': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD150': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD152': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD154': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD158': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD16': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD161': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD162': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD163': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD18': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD19': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD197': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD1d': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD2': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD20': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD200': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD22': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD229': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD244': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD25': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD26': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD268': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD27': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD274': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD278': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD279': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD29': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD314': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD32': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD328': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD33': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD337': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD35': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD36': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD37': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD38': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD3E': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD4': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD40': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD41': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD43': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD44': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD45': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD45RA': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD45RB': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD47': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD48': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD49D': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD5': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD50': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD52': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD53': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD54': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD55': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD59': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD62P': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD64': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD69': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD7': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD71': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD72': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD8': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD82': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD84': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD86': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD9': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'HLA-ABC': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'HLA-DR': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'TCRb': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'mIgG1': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'mIgG2a': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'mIgG2b': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
dpa_markers
#> # A tibble: 80 × 14
#>      estimate data_type target  reference    n1    n2 statistic     p p_adj
#>         <dbl> <chr>     <chr>   <chr>     <int> <int>     <dbl> <dbl> <dbl>
#>  1  0         morans_z  Sample1 Sample2       4     4       8       1     1
#>  2  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  3  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  4 -0.0000610 morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  5  0         morans_z  Sample1 Sample2       4     4       8       1     1
#>  6  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  7  0.0000256 morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  8  0         morans_z  Sample1 Sample2       3     3       4.5     1     1
#>  9  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#> 10  0.0000178 morans_z  Sample1 Sample2       5     5      12.5     1     1
#> # ℹ 70 more rows
#> # ℹ 5 more variables: conf.low <dbl>, conf.high <dbl>, method <chr>,
#> #   alternative <chr>, marker <chr>

# Seurat objects
seur1 <- seur2 <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins
seur1$sample <- "Sample1"
seur2$sample <- "Sample2"
seur_merged <- merge(seur1, seur2, add.cell.ids = c("A", "B"))

# Run DPA
dpa_markers <- RunDPA(seur_merged,
  contrast_column = "sample",
  targets = "Sample1", reference = "Sample2"
)
#> ℹ Splitting data by: marker
#> ℹ Polarity metric: 'morans_z'
#> ℹ Running 80 tests for the following comparison:
#>   - Sample1 vs Sample2
#> Warning: Got the following message when running wilcox.test test for marker 'ACTB': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'B2M': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD102': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD11a': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD11b': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD11c': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD127': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD137': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD14': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD150': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD152': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD154': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD158': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD16': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD161': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD162': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD163': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD18': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD19': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD197': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD1d': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD2': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD20': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD200': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD22': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD229': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD244': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD25': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD26': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD268': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD27': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD274': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD278': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD279': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD29': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD314': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD32': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD328': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD33': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD337': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD35': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD36': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD37': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD38': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD3E': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD4': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD40': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD41': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD43': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD44': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD45': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD45RA': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD45RB': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD47': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD48': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD49D': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD5': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD50': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD52': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD53': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD54': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD55': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD59': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD62P': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD64': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD69': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD7': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD71': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD72': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD8': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD82': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD84': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD86': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'CD9': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'HLA-ABC': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'HLA-DR': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'TCRb': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'mIgG1': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'mIgG2a': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
#> Warning: Got the following message when running wilcox.test test for marker 'mIgG2b': Sample1 vs Sample2
#>   cannot compute exact confidence intervals with ties
dpa_markers
#> # A tibble: 80 × 14
#>      estimate data_type target  reference    n1    n2 statistic     p p_adj
#>         <dbl> <chr>     <chr>   <chr>     <int> <int>     <dbl> <dbl> <dbl>
#>  1  0         morans_z  Sample1 Sample2       4     4       8       1     1
#>  2  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  3  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  4 -0.0000610 morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  5  0         morans_z  Sample1 Sample2       4     4       8       1     1
#>  6  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  7  0.0000256 morans_z  Sample1 Sample2       5     5      12.5     1     1
#>  8  0         morans_z  Sample1 Sample2       3     3       4.5     1     1
#>  9  0         morans_z  Sample1 Sample2       5     5      12.5     1     1
#> 10  0.0000178 morans_z  Sample1 Sample2       5     5      12.5     1     1
#> # ℹ 70 more rows
#> # ℹ 5 more variables: conf.low <dbl>, conf.high <dbl>, method <chr>,
#> #   alternative <chr>, marker <chr>