compute_gene_meth_profile: compute_gene_meth_profile

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

compute_gene_meth_profile

Description

Generate differential methylation profile for a gene around the transcription start side

Usage

compute_gene_meth_profile(gene, exp_grp, data_meth, pf_meth, type_of_analysis,
  contrast = c("tissue_status", "patho", "normal"),
  indiv_filtering_matrix = NULL, pf_pos_colname, pf_chr_colname, updwn_str,
  slide, wig_size, mask_wide, apply_func = apply, min_DE_samples = 5)

Arguments

gene	A list that describe gene in bed format.
exp_grp	A exp_grp dataframe that contains metadatas on individuals and samples.
data_meth	A matrix of row methylation data with TCGA sample ids as column names and probes ids as row names.
pf_meth	a data.frame with metadata types as columns names and probes ids as row names.
type_of_analysis	A string indicating if you want to make a population or an individual analysis. Could either be "pop" or "indiv". If not specifyed, all samples are take.
contrast	A vector containing the constrast to use to estimate the compute the methylation profiles. Required if you are in the "pop" mode.
indiv_filtering_matrix	A matrix of filter to define reference and tested individual for each probe. Required if you are in the "indiv" mode.
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 information of probes
updwn_str	is the width of the window on the chromosome in bp where the function will fetch probes position and differential methylation value
slide	is the maximum width slide you'll alow when comparing two curve
wig_size	is resolution at which the function interpolate the probes signal
mask_wide	is mask wide of o probe
apply_func	Function that will be used for apply.
min_DE_samples	A minimum of differentially expressed sample to consider a given gene as suitable for further analysis. Required if you are in the "indiv" mode.

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