lmFitComp: lmFitComp

In alrein05/lmFitComp:

Description

Takes a beta matrix of methylation data, a phenotype data frame with variables of interest, and a designation of which column number in the phenotype data contains the variable for which we are investigating differential methylation. It returns the number of CpG sites in the genome that are hyper-methylated, hypo-methylated or not significant. Also returns per-probe log fold change, t-statistics, and p-values.

Usage

lmFitComp(beta, pheno, colNum)

Arguments

beta	A matrix of beta-values between 0 and 1 with columns as samples and rows as probes
pheno	A phenotype data frame containing variables of interest on samples. Must be ordered the same as beta matrix.
colNum	An integer denoting the column number of the pheno data that contains the variable of interest

Value

number of hypomethylated sites (down), insignificant sites, and hypermethylated sites (up) as well as the log fold change, t-statistic, p-values and adjusted p-values per probe

Examples

lmFitComp(beta_matrix, phenotype_dataframe)

alrein05/lmFitComp documentation built on Dec. 19, 2021, 1:36 a.m.