estimateLeukocyte: Estimate leukocyte fraction using a two-component model

Description Usage Arguments Value Examples

View source: R/cell_composition.R

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

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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

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

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