compute_indiv_dm_table: Compute differential mehylation table for each probe...

In magrichard/dmprocr: A R package that performs differential methylation profiles clustering

Compute differential mehylation table for each probe according to individual-level analysis.

Description

Generate differential methylation data table from beta values. According to a reference individual matrix which indicates which samples should be considere as reference for a given probe, the function computes the methylation difference between each tested sample and the mean of reference samples.

Usage

compute_indiv_dm_table(gene_list, exp_grp, data_meth,
  filter_indiv = "no_filter", indiv_filtering_matrix, pf_meth, pf_pos_colname,
  pf_chr_colname, updwn_str = 5000, slide = 0, apply_func = apply,
  contrast = c("tissue_status", "patho", "normal"), reference = "normal",
  probe_idx)

Arguments

gene_list	A gene_list bedfile containing the genes to screen for differential methylation.
exp_grp	A exp_grp dataframe that contains metadatas on individuals and samples.
data_meth	A meth matrix that contains methylation information (beta values). Columns correspond to indivuals, row correspond to probes.
filter_indiv	A vector of individual names to be screened for differential methylation. Optionnal (set on "no_filter" by default).
indiv_filtering_matrix	A matrix of filter to define differentially expressed gene for each pathological sample for each probe. Rownames should be contained in rownames(gene_list) and colnames should contain filter_indiv. Reference individuals should be set to "0" and individuals to be tested should be set to "1".
pf_meth	A data frame describing CpG positions.
pf_pos_colname	String matching the name of the column in the platform that contain the position information of probes.
pf_chr_colname	String matching the name of the column in the platform that contain the chromosome on which we find a probes.
updwn_str	An integer specifying up and down stream size (in bp). By default set on 5000pb.
slide	The maximum width slide allowed when comparing two curves. By default set on 0.
apply_func	A function to be used as/instead of R base::apply. By default set on base::apply.
contrast	A vector containing the constrast to use to estimate the compute the methylation profiles. Required if you are in the "pop" mode.
reference	A string indicating what sample to considere as reference. Should be "normal" or "no_de" for all samples without differential expression (normal + patho).
probe_idx	A list of probes associated with each gene

Value

A matrix of differential methylation values based on single individual analysis.

magrichard/dmprocr documentation built on July 21, 2023, 11:01 p.m.