importData_soGGi: Import the data from bam files directly

In DChIPRep: DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

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.

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.

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)

DChIPRep documentation built on April 29, 2020, 4:26 a.m.