buildInput {uncoverappLib} | R Documentation

## Build input file

### 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)

[Package uncoverappLib version 1.0.0 Index]