makeSummarizedExperimentFromCountMatrix: Make Summarized Experiment object from raw or normalised...
In kauralasoo/eQTLUtils:

View source: R/SummarizedExperiment_helpers.R

makeSummarizedExperimentFromCountMatrix

R Documentation

Make Summarized Experiment object from raw or normalised count matrix

Description

Make Summarized Experiment object from raw or normalised count matrix

Usage

makeSummarizedExperimentFromCountMatrix(
  assay,
  row_data,
  col_data,
  assay_name = "counts",
  quant_method = "gene_counts",
  reformat = TRUE
)

Arguments

`assay`	count matrix of any phenotype quantification.
`row_data`	phenotype metadata
`col_data`	sample metadata
`assay_name`	custom assay name to be created in SE. Default "counts"
`quant_method`	Quantification method. Can be gene_counts, leafcutter, txrevise, transcript_usage or exon_counts
`reformat`	Reformat phenotype ids. Default TRUE.