process_diff_beatson: Process differential BS-Seq and RNA-Seq Beatson HTS data
In andreaskapou/processHTS: Process HTS Files and Data

Description Usage Arguments Value Examples

process_diff_beatson is a wrapper method ...

process_diff_beatson(bs_contr_files, bs_treat_files, rna_contr_files,
  rna_treat_files, chrom_size_file = NULL, chr_discarded = NULL,
  upstream = -100, downstream = 100, min_bs_cov = 0, max_bs_cov = 1000,
  cpg_density = 1, sd_thresh = 0, ignore_strand = FALSE, fmin = -1,
  fmax = 1)

`bs_contr_files`	The name of the control BS-Seq '.bed' formatted files to read data values from.
`bs_treat_files`	The name of the treatment BS-Seq '.bed' formatted files to read data values from.
`rna_contr_files`	The name of the control RNA-Seq '.bed' formatted files to read data values from.
`rna_treat_files`	The name of the treatment RNA-Seq '.bed' formatted files to read data values from.
`chrom_size_file`	Optional name of the file containing genome chromosome sizes
`chr_discarded`	A vector with chromosome names to be discarded.
`upstream`	Integer defining the length of bp upstream of TSS.
`downstream`	Integer defining the length of bp downstream of TSS.
`min_bs_cov`	The minimum number of reads mapping to each CpG site.
`max_bs_cov`	The maximum number of reads mapping to each CpG site.
`cpg_density`	Optional integer defining the minimum number of CpGs that have to be in a methylated region. Regions with less than `n` CpGs are discarded.
`sd_thresh`	Optional numeric defining the minimum standard deviation of the methylation change in a region. This is used to filter regions with no methylation change.
`ignore_strand`	Logical, whether or not to ignore strand information.
`fmin`	Optional minimum range value for region location scaling. Under this version, this parameter should be left to its default value.
`fmax`	Optional maximum range value for region location scaling. Under this version, this parameter should be left to its default value.

A diff_processHTS object which contains among others the following information:

methyl_region: A list containing the methylation regions, where each each entry in the list consists of an L X 3 dimensional matrix, where:
1. 1st col: Contains the locations of the CpGs relative to TSS, where the range (min, max) of possible values is given, by the inputs fmin and fmax.
2. 2nd col: The total reads of the CpG in the corresponding location.
3. 3rd col: The methylated reads of the CpG in the corresponding location.
prom_region: A GRanges object containing corresponding annotated promoter regions for each entry of the methyl_region list..
rna_data: A GRanges object containing the corresponding RNA-Seq data for each entry of the methyl_region list.

# Get the location of the files
bs_file <- system.file("extdata", "bism_rep1.bed", package = "processHTS")
rna_file <- system.file("extdata", "rna_beatson.bed", package = "processHTS")
#data <- process_beatson(bs_file, rna_file)