Extract CAGE Transcription Start Sites (CTSSs) from BigWig Files

This function extracts CTSSs from CAGE data stored in BigWig files, as specified in the provided design matrix. It allows for optional genomic filtering based on a provided `Seqinfo` object and can exclude or include specific chromosomes.

Usage

plc_get_ctss_from_bw(
  dir_cage_bw,
  design_matrix,
  genome_info = NULL,
  drop_chr = NULL,
  keep_chr = NULL
)

Arguments

dir_cage_bw: A character string specifying the directory containing the BigWig files for both plus and minus strands.
design_matrix: A data frame that must contain columns named "BigWigPlus" and "BigWigMinus", which specify the paths to the respective BigWig files.
genome_info: An optional Seqinfo object containing genome information. If provided, it allows for the use of `drop_chr` and `keep_chr` parameters.
drop_chr: An optional character vector of chromosome names to be excluded from the analysis. Requires genome_info to be specified.
keep_chr: An optional character vector of chromosome names to be included in the analysis. Requires genome_info to be specified.

Value

A CTSS object containing the quantified and normalized counts of transcription start sites, including pooled counts.

Examples

if (FALSE) { # \dontrun{
ctss_result <- plc_get_ctss_from_bw("path/to/bigwig/files",
                                    design_matrix,
                                    genome_info,
                                    drop_chr = c("chrM"))
} # }