estimateLeukocyte {sesame} | R Documentation

## Estimate leukocyte fraction using a two-component model

### 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)

[Package sesame version 1.12.9 Index]