makeInputMatrix: Make input matrix

In HengPan2007/MethSig: DNA Methylation Drivers Inference

Description

Add DHcR, PDR and sequencing depth information of inferred samples into the input matrix.

Usage

makeInputMatrix(names_list, matCV, pro, input_dir, min_cpgs = c(5, 3))

Arguments

names_list	A list of sample names.
matCV	A matrix of covariates included in the analysis. Ideally, users can include any covariate and a hugo symbol column. An example can be loaded by using invisible(matCV). This covariate matrix contains following columns: Hugo, DHcR_Normal, PDR_Normal, GEXP_Normal, Reptime.
pro	A GRanges object containing promoter annotation.
input_dir	A string indicating where input files used to calculate DHcR and PDR are stored. Input files used to calculate DHcR should be named as DMC.sample_name.txt. Input files used to calculate PDR should be named as PDR.sample_name.txt.
min_cpgs	A list of two integer values: the minimum number of CpGs requied by promoterDHcR and the minimum number of CpGs required by promoterPDR.

Value

A data frame used as input for sample-specific hypermethylation inference.

• Id: Sample id

• Hugo: Hugo symbol

• Covariates included in matCV

• PDR_Tumor: PDR level in tumor samples

• Depth_Tumor: Average sequencing depth in tumor samples

• CpGs_Tumor: Number of CpGs covered in tumor samples

• DHcR_Tumor: DHcR level in tumor samples

Examples

makeInputMatrix(names_list = as.list("SRR2069925"),
                matCV = invisible(matCV),
                pro = makeHG19Promoters(),
                input_dir = system.file("extdata", "", package = "MethSig"))

HengPan2007/MethSig documentation built on Aug. 1, 2020, 4:52 a.m.