estimateLeukocyte: Estimate leukocyte fraction using a two-component model

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

The method assumes only two components in the mixture: the leukocyte component and the target tissue component. The function takes the beta values matrix of the target tissue and the beta value matrix of the leukocyte. Both matrices have probes on the row and samples on the column. Row names should have probe IDs from the platform. The function outputs a single numeric describing the fraction of leukocyte.

Usage

estimateLeukocyte(
  betas.tissue,
  betas.leuko = NULL,
  betas.tumor = NULL,
  platform = c("EPIC", "HM450", "HM27")
)

Arguments

betas.tissue	tissue beta value matrix (#probes X #samples)
betas.leuko	leukocyte beta value matrix, if missing, use the SeSAMe default by infinium platform
betas.tumor	optional, tumor beta value matrix
platform	"HM450", "HM27" or "EPIC"

Value

leukocyte estimate, a numeric vector

Examples

betas.tissue <- sesameDataGet('HM450.1.TCGA.PAAD')$betas
estimateLeukocyte(betas.tissue)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.