analyse_meth: A Function Analyses Methylome data

Description Usage Arguments Value Examples

Description

This function analyses methylome data.

Usage

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analyse_meth(gene, meth_data, meth_platform, probe_idx,
  pf_chr_colname = "Chromosome", pf_pos_colname = "Start", PLOT = TRUE,
  up_str = 5000, dwn_str = 5000, win_size = 1500, wig_size = 50,
  JUST_PROBE_POS = FALSE, GAUSSIAN_MIXTURE = TRUE, mat_mult = function(A,
  B) {     A %*% B })

Arguments

gene

A vector describing the gene (line of a bed file).

meth_data

A matrix of beta values.

meth_platform

A data frame describing CpG positions.

probe_idx

A vector specifying probes associated to the gene.

pf_chr_colname

string matching the name of the column in the platform that contain the chromosome on which we find a probes.

pf_pos_colname

string matching the name of the column in the platform that contain the position information of probes.

PLOT

A boolean defining if graphical output must be dispayed on the graphical output.

up_str

An integer specifying up stream size (in bp).

dwn_str

An integer specifying down stream size (in bp).

win_size

An integer specifying slidding window size (in bp).

wig_size

An integer specifying wiggle size (in bp).

JUST_PROBE_POS

A boolean defining if function returns only probes positions.

GAUSSIAN_MIXTURE

A boolean specifying if gaussian mixture model is use to convolve signal.

mat_mult

A function to multiply matrices.

Value

A matrix of convolved probes signal around the TSS of the selected gene.

Examples

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cols = as.numeric(sunexp_design$sex) * 2
names(cols) = rownames(sunexp_design)
gene = genes[1,]
res1 = analyse_meth(gene, sunexp_data, sunexp_platform)
plot_meth(res1, cols)
legend("topright", col=as.numeric(unique(sunexp_design$sex)) * 2, 
       legend=unique(sunexp_design$sex), lty=1)

fchuffar/methmybeachup documentation built on May 16, 2019, 12:07 p.m.