TransAct: A TransAct function

In prodakt/lncRna: Long Non-coding RNA Identification

A TransAct function

Description

This function allows to estimate trans interactions between lncRNA's and potential target genes basing on the expression/coexpression levels. This function requires the "Hmisc" library to be installed

Usage

TransAct(
  expr.matrix,
  cor.method = "pearson",
  rval = 0.7,
  pval = 0.05,
  lncRNA.list = NULL,
  tarRNA.list = NULL,
  full.cor.matrix.filename = NULL
)

Arguments

expr.matrix	espression matrix; rownames should contains the genes or transcripts names and collumns shoud be the samples.
cor.method	correlation metthod: "pearson" or "spearman"
rval	the cutoff of correlation coeficient; default value is 0.7
pval	the cutoff of estimated p-value for any interaction; default value is 0.05
lncRNA.list	the list of lncRNA genes/transcripts. The manes shoud be a part of "expr.matrix" rownames.
tarRNA.list	the list of target genes/transcripts. The manes shoud be a part of "expr.matrix" rownames.
full.cor.matrix.filename	the filename of precalculated corelation matrix

Examples

transNjJd <- TransAct(expr.matrix = em_NjJd, rval = 0.9, lncRNA.list = DELsNjJd, tarRNA.list = pcDEGsNjJd)
head(transNjJd)
TransAct()

prodakt/lncRna documentation built on June 1, 2025, 1:05 p.m.