tallyBAM {h5vc} | R Documentation |
Function for creating tallies from bam files.
tallyBAM(file, chr, start, stop, q=25, ncycles = 0, max.depth=1000000, verbose=FALSE, reference = NULL)
file |
filename of the BAM file that should be tallies |
chr |
Chromosome in which to tally |
start |
First position of the tally |
stop |
Last position of the tally |
q |
quality cut-off for considering a base call |
ncycles |
number of sequencing cycles form the front and back of the read that should be considered unreliable |
max.depth |
only tally a position if there are less than this many reads overlapping it - can prevent long runtimes in unreliable regions |
verbose |
should additional information be printed |
reference |
|
This function tallies nucleotides and deletion counts in the specified region of a given BAM file. The results can be processed with the prepareForHDF5
function.
This function was adapted from the bam2R
function provided by the deepSNV
package.
An array object with dimensions [stop - start + 1, 18, 2]
which represent positions times nucleotides (4 bases + deletions + insertions times three for early, middle and late sequencing cycles) times strands.
Paul Pyl
library(h5vc) files <- c("NRAS.AML.bam","NRAS.Control.bam") bamFiles <- file.path( system.file("extdata", package = "h5vcData"), files) chrom = "1" startpos <- 115247090 endpos <- 115259515 theData <- lapply( bamFiles, function(bamf){ tallyBAM( file = bamf, chr = chrom, start = startpos, stop = endpos, ncycles = 10 ) }) str(theData) print(theData[[1]][,,,9491]) #position 9491 of the pileup