buildInput: Build input file

In uncoverappLib: Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Description

Function to build input file for unCOVERAPP when the number of genes to analyze is > 50.

Usage

buildInput(
  geneList,
  genome,
  type_bam,
  bamList,
  outDir,
  MAPQ.min = 1,
  base.quality = 1
)

Arguments

geneList	a text file, named with .txt extension, containing HGNC official gene name(s) one per row.
genome	(char) reference genome, hg19 or hg38
type_bam	(char) chromosome notation of their BAM file(s). Use "number" or "chr". In the BAM file, the number option refers to 1, 2, ..., X,.M chromosome notation, while the chr option refers to chr1, chr2, ... chrX, chrM chromosome notation.
bamList	a text file, named with .list extension, containing the absolute paths to BAM file(s) one per row.
outDir	(char) directory where pileup output will be stored
MAPQ.min	(integer) minimum MAPQ value for an alignment to be included in output file.
base.quality	(integer) minimum QUAL value for each nucleotide in an alignment.

Value

A file.bed containing tab-separated specifications of genomic coordinates (chromosome, start position, end position), the coverage value, and the reference:alternate allele counts for each position.

Examples

gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib")

bam_example <- system.file("extdata", "example_POLG.bam",
package = "uncoverappLib")
cat(bam_example, file = "bam.list", sep = "\n")
temp_dir=tempdir()
buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr",
bamList= "bam.list", outDir= temp_dir)

uncoverappLib documentation built on Nov. 8, 2020, 5:07 p.m.