process_bismark_beatson_wrap: Wrapper method for processing ENCODE HAIB and Caltech HTS...
In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles

Description Usage Arguments Value Author(s)

process_bismark_beatson_wrap is a wrapper method for processing HTS data and returning the methylation promoter regions and the corresponding gene expression data for those promoter regions. Note that the format of BS-Seq data should be in the bismark format and for the RNA-Seq data in Beatson bed format.

process_bismark_beatson_wrap(bs_files, rna_files, chrom_size_file = NULL,
  chr_discarded = NULL, upstream = -7000, downstream = 7000,
  min_bs_cov = 4, max_bs_cov = 1000, cpg_density = 10, sd_thresh = 0.1,
  ignore_strand = TRUE, gene_log2_transf = TRUE, gene_outl_thresh = TRUE,
  gex_outlier = 300, fmin = -1, fmax = 1)

`bs_files`	Filename (or vector of filenames if there are replicates) of the BS-Seq '.bed' formatted data to read values from.
`rna_files`	Filename of the RNA-Seq '.bed' formatted data to read values from. Currently, this version does not support pooling RNA-Seq replicates.
`chrom_size_file`	Optional filename containing genome chromosome sizes.
`chr_discarded`	A vector with chromosome names to be discarded.
`upstream`	Integer defining the length of bp upstream of TSS for creating the promoter region.
`downstream`	Integer defining the length of bp downstream of TSS for creating the promoter region.
`min_bs_cov`	The minimum number of reads mapping to each CpG site. CpGs with less reads will be considered as noise and will be discarded.
`max_bs_cov`	The maximum number of reads mapping to each CpG site. CpGs with more reads will be considered as noise and will be discarded.
`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.
`gene_log2_transf`	Logical, whether or not to log2 transform the gene expression data.
`gene_outl_thresh`	Logical, whehter or not to remove outlier gene expression data.
`gex_outlier`	Numeric, denoting the threshold above of which the gene expression data (before the log2 transformation) are considered as noise.
`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 processHTS object which contains following information:

methyl_region: A list containing methylation data, where each entry in the list is an L_{i} X 3 dimensional matrix, where L_{i} denotes the number of CpGs found in region i. The columns contain the following information:
1. 1st column: Contains the locations of CpGs relative to TSS. Note that the actual locations are scaled to the (fmin, fmax) region.
2. 2nd column: Contains the total reads of each CpG in the corresponding location.
3. 3rd column: Contains the methylated reads each CpG in the corresponding location.
gex: A vector containing the corresponding gene expression levels for each entry of the methyl_region list.
prom_region: A GRanges object containing corresponding annotated promoter regions for each entry of the methyl_region list. The GRanges object has one additional metadata column named tss, which stores the TSS of each promoter.
rna_data: A GRanges object containing the corresponding RNA-Seq data for each entry of the methyl_region list. The GRanges object has three additional metadata columns which are explained in read_rna_encode_caltech
upstream: Integer defining the length of bp upstream of TSS.
downstream: Integer defining the length of bp downstream of TSS.
cpg_density: 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: Numeric defining the minimum standard deviation of the methylation change in a region. This is used to filter regions with no methylation change.
fmin: Minimum range value for region location scaling.
fmax: Maximum range value for region location scaling.