mapCaps {icetea} | R Documentation

## Map the data from 5' profiling techniques

### Description

Map the data from 5' profiling techniques

### Usage

    mapCaps(
      CSobject,
      genomeIndex,
      outdir,
      externalGTF = NULL,
      ncores = 1,
      logfile = NULL
    )

    ## S4 method for signature 'CapSet'
    mapCaps(
      CSobject,
      genomeIndex,
      outdir,
      externalGTF = NULL,
      ncores = 1,
      logfile = NULL
    )

### Arguments

`CSobject` | An object of class `CapSet`
`genomeIndex` | character. Path to the Subread index file. Should end with the basename of the index.
`outdir` | character. Output directory path
`externalGTF` | character. provide external annotation file in 'GTF' format , if present to increase alignment accuracy
`ncores` | integer. Number of cores/threads to use for mapping.
`logfile` | character. A log file to write the processing message.

### Value

modified CapSet object with mapping information. Mapped and sorted BAM files are saved in 'outdir'.

### Examples

    ## Not run:
    # before mapping :
    # 1. Create a CapSet object
    # 2. de-multiplex the fastqs

    # load a previously saved CapSet object
    cs <- exampleCSobject()

    # map the data (not available on windows)
    library(Rsubread)
    dir.create("bam")
    buildindex(basename = "dm6", reference = "/path/to/dm6_genome.fa")
    cs <- mapCaps(cs, genomeIndex = "dm6", outdir = "bam", nthreads = 10)

    ## End(Not run)

[Package icetea version 1.8.0 Index]