preprocess_final_HTS_data: (DEPRECATED) Pre-process final HTS data for downstream...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/deprecated_process_functions.R

Description

(DEPRECATED) preprocess_final_HTS_data performs a final filtering and preprocessing on the data for use in downstream analysis. These include, removing noisy gene expression data, removing or not un-expressed genes and log2-transorming of the FPKM values.

Usage

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preprocess_final_HTS_data(
  methyl_region,
  prom_reg,
  rna_data,
  gene_log2_transf = TRUE,
  gene_outl_thresh = TRUE,
  gex_outlier = 300
)

Arguments

methyl_region

Methylation region data, which are the output of the "create_region_object" function.

prom_reg

A GRanges object containing corresponding annotated promoter regions for each entry of the methyl_region list.

rna_data

A GRanges object containing corresponding RNA-Seq data for each entry of the methyl_region list. This is the output of the "read_rna_encode_caltech function.

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.

Value

An object which contains following information:

Author(s)

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

See Also

read_rna_encode_caltech process_haib_caltech_wrap

Examples

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# Obtain the path to the BS file and then read it
bs_file <- system.file("extdata", "rrbs.bed", package = "BPRMeth")
bs_data <- read_bs_encode_haib(bs_file)

# Create promoter regions
rnaseq_file <- system.file("extdata", "rnaseq.bed", package = "BPRMeth")
annot_data <- read_rna_encode_caltech(rnaseq_file)
prom_region <- create_anno_region(annot_data)

# Create methylation regions
methyl_reg <- create_region_object(bs_data, prom_region,
  filter_empty_region = FALSE)

# Keep only covered genomic regions
cov_ind <- which(!is.na(methyl_reg))
methyl_reg <- methyl_reg[cov_ind]
prom_region <- prom_region[cov_ind, ]
annot_data <- annot_data[cov_ind, ]

# Finally preprocess the HTS data
res <- preprocess_final_HTS_data(methyl_reg, prom_region, annot_data)

BPRMeth documentation built on Nov. 8, 2020, 5:54 p.m.