countSubsetNorm: RNAseq counts subsetting and normalizing.

Description Usage Arguments Details Value

View source: R/calc_norm_counts_scRNAseq.R

This function performs a number of operations on a counts object. It optionally filters out low-count genes. It optionally normalizes, log2-transforms, and/or transposes counts.

calc_norm_counts_scRNAseq(
  counts,
  min_count=NULL, min_cpm=NULL, min_libs_perc=0.15,
  normalize=TRUE, norm_method="TMM",
  log2_transform=FALSE, transpose=FALSE, return_DGEcounts=FALSE,
  ...)

`counts`	a matrix or data frame of gene expression counts. Should have samples in columns and genes in rows.
`min_count`	numeric, the minimum count for a library to be considered passing threshold for a given gene. Setting to NULL avoids filtering by minimum counts.
`min_cpm`	numeric, the minimum counts per million for a library to be considered passing threshold for a given gene. Setting to NULL avoids filtering by minimum counts.
`min_libs_perc`	numeric, the minimum percentage of libraries that must meet `min_count` or `min_cpm` threshold for a gene to be retained.
`normalize`	logical, whether to normalize counts.
`norm_method`	character, the method by which to normalize counts. Used only if `normalize` is TRUE. Options are "TMM", which uses `edgeR::calcNormFactors`; "deconvolution", which uses cell deconvolution as implemented in the package `scran`; or "lib_size", simple library size normalization using cpm. Unique partial matches are accepted.
`log2_transform`	logical, whether to log2 transform the counts. Defaults to `FALSE`.
`transpose`	logical, whether to transpose the matrix or data frame of counts.
`...`	(optional) parameters passed to normalization functions.

This function (optionally) utilizes min_filter_counts to filter the counts object. It then (optionally) normalizes the counts, using one of several methods applicable to single-cell RNA-seq data. It then (optionally) log2-transforms the counts and/or transposes the counts object. Finally, it returns the counts either as a data frame, or as a DGEList object.

a data frame containing the processed counts.

mjdufort/countSubsetNorm documentation built on Nov. 7, 2019, 6:37 p.m.