This function imports the data from .bam files directly. It will
return a matrix with one column per .bam file and the respective counts per
postion in the rows. It uses the function regionPlot
from the package
soGGi.
a character vector of paths to the bam file(s)
to be imported.
TSS
a GRanges (GenomicRanges-class) (or a class
that inherets from it)
object containing the TSS of interest.
fragment_lengths
an integer vector of fragment lengths,
sample_ids
a character vector of sample ids for the .bam files.
This can also be a factor.
distanceUp
Distance upstream from centre of the TSS provided.
distanceDown
Distance downstream from centre of the TSS provided.
...
additional arguments passed to regionPlot.
Details
In the example below, we use a subsampled .bam file (0.1 % of the reads)
from the Galonska et. al. WCE (whole cell extract) H3Kme3 data and associated
TSS near identified peaks. For additional details on the data,
see input_galonska
and TSS_galonska.
Value
a matrix that contains the postion-wise profiles per .bam
file in the colmuns.