estimateMedianTPM: Estimate median TPM for each gene in each sample group of a...

In kauralasoo/eQTLUtils:

Estimate median TPM for each gene in each sample group of a SummarizedExperiment object.

Description

Sample groups are defined accroding to the subset_by column of the colData data frame. The prob parmeter can be modified to estimate anu other quantile of the distribution.

Usage

estimateMedianTPM(
  se,
  subset_by = "qtl_group",
  assay_name = "counts",
  prob = 0.5
)

Arguments

se	SummarizedExperiment object
subset_by	Name of the column used for subsetting the data.
assay_name	Name of the assay used for TPM normalisation and calculation of median
prob	Specifies which quantile of the dataset to calculate. Default is prob = 0.5 (median)

Value

data frame of media tpm values per gene and sample group.

kauralasoo/eQTLUtils documentation built on March 12, 2023, 8:50 p.m.