Map the data from 5' profiling techniques

Source: R/AllGenerics.R, R/mapCaps.R

Map the data from 5' profiling techniques

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

# S4 method for 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)

# }