mapCaps {icetea} | R Documentation |
Map the data from 5' profiling techniques
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)
CSobject |
An object of class |
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. |
modified CapSet object with mapping information. Mapped and sorted BAM files are saved in 'outdir'.
## 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)