pol2_index: Calculate polymerase2 pausing index for every gene according...

In ClaudiaRHD/chipAnalyser: R package for rapid ChIP-seq data analysis and visualisation.

Description

Calculate polymerase2 pausing index for every gene according to the inserted gene model file. Returns a list (name, size_tss, sum_tss, size_gb, sum_gb, geneNAme, TxName, chrom ,strand, txStart, txEnd, nr, dr, pi). With used filter duplicated and overlapping genes can be removed from list as well as non necessary columns. Returns a list (name, geneName, txName, chrom, strand, txStart, txEnd, nr, dr, pi, dif).

Usage

pol2_index(gm = NULL, bw_files = NULL, bw_path = NULL, op_dir = NULL,
  filter = TRUE, numcores = NULL)

Arguments

gm	Gene model. File with information about the transcription start and end position of every gene. Default value is NULL.
bw_files	One or a character vector with multiple files in bigWig format. Default value is NULL.
bw_path	The path to directory where bwtool is installed on the computer. Default value is NULL.
op_dir	The path to the operation directory currently used. Default value is NULL.
filter	Filter which can be used to filter the output list to remove duplicated and overlapping genes as well as non necessary columns. Default value is TRUE.
numcores	Number of cores which should be used in parallelised process.Default value is NULL and will be defined as the number of available cores - 1.

Value

list (name, size_tss, sum_tss, size_gb, sum_gb, geneNAme, TxName, chrom ,strand, txStart, txEnd, nr, dr, pi). IF filter = TRUE : list (name, geneName, txName, chrom, strand, txStart, txEnd, nr, dr, pi, dif)

ClaudiaRHD/chipAnalyser documentation built on June 18, 2020, 8:31 p.m.