cisInter: cisInter function This function reads several outputs from...

In prodakt/lncRna: Long Non-coding RNA Identification

cisInter function This function reads several outputs from coding potential programs and join all tesults in table, where 0 is coding and 1 - noncoding

Description

cisInter function This function reads several outputs from coding potential programs and join all tesults in table, where 0 is coding and 1 - noncoding

Usage

cisInter(
  lncRNAs = NULL,
  mRNAs = NULL,
  FEELnc.classes,
  is.best = T,
  lncRNA.level = "transcript",
  mRNA.level = "gene",
  max.dist = 1e+05
)

Arguments

lncRNAs	the list of lncRNA IDs (genes or transcripts)
mRNAs	the list of mRNA IDs (genes or transcripts)
FEELnc.classes	the "classes" output file from FEELnc
is.best	filtering by the first collumn "is.best" (see https://github.com/tderrien/FEELnc)
lncRNA.level	choose the "gene" or "transcript" level for lncRNA filtering
mRNA.level	choose the "gene" or "transcript" level for mRNA filtering
max.dist	the distance for cis-relation (default value is 100 000)

Examples

cisInter()

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