riboSeqR (version 1.6.0)

readRibodata: Reads ribosomal and (optionally) rna data from alignment files.

Description

Reads BAM files, or flat text files (which may be compressed) containing strand, transcript name, start and sequence information for each alignment.

Usage

readRibodata(riboFiles, rnaFiles, columns = c(strand = 1, seqname = 2,
start = 3, sequence = 4), zeroIndexed = TRUE, header = FALSE, replicates, seqnames)

Arguments

riboFiles

Filenames of ribosomal alignments.

rnaFiles

Filenames of RNA alignments.

columns

Columns of alignment files containing strand, transcript (seqname) name, start of alignment, and sequence. Ignored for BAM files.

zeroIndexed

Are the alignments zero-indexed (i.e., the first base in a sequence is 0). Defaults to TRUE, which will result in an adjustment to 1-indexed data.

header

Does the alignment file have a header line? Defaults to FALSE.

replicates

Replicate information for the files.

seqnames

Transcript (seqname) names to be read into the object.

Value

riboData object.

Details

If a filename ends in '.bam' or '.BAM' it will be assumed that the file is a BAM file and processed accordingly. Otherwise, it will be treated as a flat text file.

Examples

datadir <- system.file("extdata", package = "riboSeqR")
ribofiles <- paste(datadir, 
                   "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
rnafiles <- paste(datadir, 
                  "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")

riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))