preAssociationProbeFiltering: Filtering probes

Description Usage Arguments Value References Examples

View source: R/Small.R

Description

This function has some filters to the DNA methylation data in each it selects probes to avoid correlations due to non-cancer contamination and for additional stringency.

Usage

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preAssociationProbeFiltering(data, K = 0.3, percentage = 0.05)

Arguments

data

A MultiAssayExperiment with a DNA methylation martrix or a DNA methylation matrix

K

Cut off to consider probes as methylated or unmethylated. Default: 0.3

percentage

The percentage of samples we should have at least considered as methylated and unmethylated

Value

An object with the same class, but with the probes removed.

References

Yao, Lijing, et al. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome biology 16.1 (2015): 1. Method section (Linking enhancer probes with methylation changes to target genes with expression changes).

Examples

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 random.probe <- runif(100, 0, 1)
 bias_l.probe <- runif(100, 0, 0.3)
 bias_g.probe <- runif(100, 0.3, 1)
 met <- rbind(random.probe,bias_l.probe,bias_g.probe)
 met <- preAssociationProbeFiltering(data = met,  K = 0.3, percentage = 0.05)
 met <- rbind(random.probe,random.probe,random.probe)
 met <- preAssociationProbeFiltering(met,  K = 0.3, percentage = 0.05)
 data <- ELMER:::getdata("elmer.data.example") # Get data from ELMER.data
 data <- preAssociationProbeFiltering(data,  K = 0.3, percentage = 0.05)
 
 cg24741609 <- runif(100, 0, 1)
 cg17468663 <- runif(100, 0, 0.3)
 cg14036402 <- runif(100, 0.3, 1)
 met <- rbind(cg24741609,cg14036402,cg17468663)
 colnames(met) <- paste("sample",1:100)
 exp <- met
 rownames(exp) <- c("ENSG00000141510","ENSG00000171862","ENSG00000171863")
 sample.info <- S4Vectors::DataFrame(sample.type = rep(c("Normal", "Tumor"),50))
 rownames(sample.info) <- colnames(exp)
 mae <- createMAE(exp = exp, met = met, colData = sample.info, genome = "hg38") 
 mae <- preAssociationProbeFiltering(mae,  K = 0.3, percentage = 0.05)

ELMER documentation built on Nov. 1, 2018, 2:13 a.m.