DChIPRep (version 1.2.3)

importData_soGGi: Import the data from bam files directly

Description

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.

Usage

importData_soGGi(bam_paths, TSS, fragment_lengths, sample_ids, distanceUp = 1000, distanceDown = 1500, ...)

Arguments

bam_paths

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.

Value

a matrix that contains the postion-wise profiles per .bam file in the colmuns.

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.

See Also

regionPlot input_galonska TSS_galonska sample_table_galonska

Examples

## Not run: 
# data(sample_table_galonska)
# data(TSS_galonska)
# bam_dir <- file.path(system.file("extdata", package="DChIPRep"))
# wce_bam <- "subsampled_0001_pc_SRR2144628_WCE_bowtie2_mapped-only_XS-filt_no-dups.bam"
# mat_wce <- importData_soGGi(bam_paths = file.path(bam_dir, wce_bam),
#                            TSS = TSS_galonska,
#                            fragment_lengths = sample_table_galonska$input_fragment_length[1],
#                            sample_ids =  sample_table_galonska$input[1],
#                            paired = FALSE,
#                            removeDup=FALSE
# )
# head(mat_wce)
# ## End(Not run)