loadBAM {ASpli} | R Documentation |
Load BAM files into R session using a targets specification.
loadBAM(targets, cores, libType, strandMode)
targets |
A data frame containing sample, bam and experimental factors columns |
cores |
Number of processors to use |
libType |
Options are: "SE" or "PE" |
strandMode |
Options are: 0,1,2. See ?strandMode for more information |
A list of GAlignments or GAlignmentPairs . Each element of the list correspond to a samples BAM file.
Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz
# Define bam files, sample names and experimental factors for targets. #bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam", # "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" ) #targets <- data.frame( # row.names = paste0('Sample_',c(1:6)), # bam = system.file( 'extdata', bamFileNames, package="ASpli" ), # factor1 = c( 'C','C','C','D','D','D') ) # Load reads from bam files #bams <- loadBAM( targets )