aqtl-methods: Inference of aQTL

In diggit: Inference of Genetic Variants Driving Cellular Phenotypes

Description

This function infers aQTLs from F-CNVs and VIPER activity

Usage

aqtl(x, ...)

## S4 method for signature 'diggit'
aqtl(x, mr = 0.01, mr.adjust = c("none", "fdr",
  "bonferroni"), fcnv = 0.01, fcnv.adjust = c("none", "fdr", "bonferroni"),
  method = c("spearman", "mi", "pearson", "kendall"), mindy = FALSE,
  cores = 1, verbose = TRUE)

Arguments

x	Object of class diggit
...	Additional parameters to pass to the function
mr	Either a numerical value between 0 and 1 indicating the p-value threshold for the Master Regulator (MR) selection, or a vector of character strings listing the MRs
mr.adjust	Character string indicating the multiple hypothesis test correction for the MRs
fcnv	Either a numerical value between 0 and 1 indicating the p-value threshold for the F-CNV, or a vector of character strings listing the F-CNVs
fcnv.adjust	Character string indicating the multiple hypothesis test correction for the F-CNVs
method	Character string indicating the method for computing the association between F-CNV and regulator activity (aQTL analysis)
mindy	Logical, whether only post-translational modulators of each evaluated TF should be considered as putative genetic driver
cores	Integer indicating the number of cores to use (1 for Windows-based systems)
verbose	Logical, whether progress should be reported

Value

Updated diggit object with viper and aqtl slots

Examples

data(gbm.expression, package="diggitdata")
data(gbm.cnv, package="diggitdata")
data(gbm.aracne, package="diggitdata")
dobj <- diggitClass(expset=gbmExprs, cnv=gbmCNV, regulon=gbmTFregulon)
dobj <- fCNV(dobj)
dobj <- aqtl(dobj, mr=c("CEBPD", "STAT3"), fcnv.adjust="fdr")
dobj
diggitAqtl(dobj)[, 1:4]

diggit documentation built on Nov. 8, 2020, 8:18 p.m.