diggit (version 1.4.0)

aqtl: Inference of aQTL

Description

This function infers aQTLs from F-CNVs and VIPER activity

Usage

aqtl(x, ...)
"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]