convertBAM2BigWig {CAGEfightR} | R Documentation

## Extract CTSSs from BAM-files (EXPERIMENTAL)

### Description

Function for converting mapped reads in BAM-files to CAGE Transcription Start Sites (CTSSs) in BigWig-files. Currently, this function will simply load a (single-end) BAM-file (respecting a supplied ScanBamParam), optionally remove short tags, and count the number of 5'-ends at each bp. Note, the BAM-file is loaded as a single object, so you must be able to keep at least one complete BAM-file in RAM.

### Usage

    convertBAM2BigWig(input, outputPlus, outputMinus, minLength = 1L, ...)

### Arguments

`input` | character: Path to input BAM-file
`outputPlus` | character: Path to output BigWig-file holding CTSSs on the plus strand.
`outputMinus` | character: Path to output BigWig-file holding CTSSs on the minus strand.
`minLength` | integer: Minimum length of mapped reads.
`...` | Additional arguments passed to rtracklayer::import. This will often include a ScanBamParam

### Value

Number of CTSSs/Tags returned invisibly.

### Note

WARNING: This function is experimental, has not been thoroughly tested, and will most likely significantly change in upcoming CAGEfightR version. For comments/question please go to the CAGEfightR github page.

### Examples

    # TBA

[Package CAGEfightR version 1.12.0 Index]