process_haib_caltech_wrap {BPRMeth} | R Documentation

## (DEPRECATED) Wrapper for processing ENCODE HAIB and Caltech HTS

### Description

(DEPRECATED) `process_haib_caltech_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 Encode Haib bed format and for the RNA-Seq data in Encode Caltech bed format.

### Usage

    process_haib_caltech_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
    )

### Arguments

`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.

### 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.

### Author(s)

C.A.Kapourani C.A.Kapourani@ed.ac.uk

### Examples

    # Obtain the path to the files
    rrbs_file <- system.file("extdata", "rrbs.bed", package = "BPRMeth")
    rnaseq_file <- system.file("extdata", "rnaseq.bed", package = "BPRMeth")
    proc_data <- process_haib_caltech_wrap(rrbs_file, rnaseq_file)

[Package BPRMeth version 1.14.1 Index]