getFactorMarkers: Find shared and dataset-specific markers

In rliger: Linked Inference of Genomic Experimental Relationships

Find shared and dataset-specific markers

Description

Applies various filters to genes on the shared (W) and dataset-specific (V) components of the factorization, before selecting those which load most significantly on each factor (in a shared or dataset-specific way).

Usage

getFactorMarkers(
  object,
  dataset1,
  dataset2,
  factorShareThresh = 10,
  datasetSpecificity = NULL,
  logFCThresh = 1,
  pvalThresh = 0.05,
  nGenes = 30,
  printGenes = FALSE,
  verbose = getOption("ligerVerbose", TRUE),
  factor.share.thresh = factorShareThresh,
  dataset.specificity = datasetSpecificity,
  log.fc.thresh = logFCThresh,
  pval.thresh = pvalThresh,
  num.genes = nGenes,
  print.genes = printGenes
)

Arguments

object	liger object with factorization results.
dataset1	Name of first dataset. Required.
dataset2	Name of second dataset. Required
factorShareThresh	Numeric. Only factors with a dataset specificity less than or equal to this threshold will be used. Default 10.
datasetSpecificity	Numeric vector. Pre-calculated dataset specificity if available. Length should match number of all factors available. Default NULL automatically calculates with calcDatasetSpecificity.
logFCThresh	Numeric. Lower log-fold change threshold for differential expression in markers. Default 1.
pvalThresh	Numeric. Upper p-value threshold for Wilcoxon rank test for gene expression. Default 0.05.
nGenes	Integer. Max number of genes to report for each dataset. Default 30.
printGenes	Logical. Whether to print ordered markers passing logFC, UMI and frac thresholds, when verbose = TRUE. Default FALSE.
verbose	Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.
factor.share.thresh, dataset.specificity, log.fc.thresh, pval.thresh, num.genes, print.genes	Deprecated. See Usage section for replacement.

Value

A list object consisting of the following entries:

value of \code{dataset1}	data.frame of dataset1-specific markers
shared	data.frame of shared markers
value of \code{dataset1}	data.frame of dataset2-specific markers
num_factors_V1	A frequency table indicating the number of factors each marker appears, in dataset1
num_factors_V2	A frequency table indicating the number of factors each marker appears, in dataset2

Examples

library(dplyr)
result <- getFactorMarkers(pbmcPlot, dataset1 = "ctrl", dataset2 = "stim")
print(class(result))
print(names(result))
result$shared %>% group_by(factor_num) %>% top_n(2, logFC)

rliger documentation built on Oct. 30, 2024, 1:07 a.m.