aqtl {diggit} | R Documentation |
This function infers aQTLs from F-CNVs and VIPER activity
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)
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 |
Updated diggit object with viper and aqtl slots
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]