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)

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