exp_environ_missingness: Expression matrix (in environ object) missingness evaluation

In alexandruioanvoda/gwascelltyper: Fast GWAS Enrichment Testing

Expression matrix (in environ object) missingness evaluation

Description

Warning: this function modifies any object it is given. This function does two things at once: 1. automatically removes completely-NA rows and columns. 2. finds out if some rows or columns have more missingness than a threshold (default = 0.1 (otherwise written, 10%)), and eliminates them (if requested).

Usage

exp_environ_missingness(
  obj,
  col_max_miss = 0.1,
  row_max_miss = 0.1,
  elim = TRUE,
  verbose = TRUE
)

Arguments

obj	Environment object containing an exp (numeric matrix of genes-by-cell-ID) & an annot (dataframe of cell annotations).
col_max_miss	Column maximum missingness (default = 0.1)
row_max_miss	Row maximum missingness (default = 0.1)
elim	Whether to eliminate rows & cols with too many NAs (default = TRUE), alternative is to just throw a warning.
verbose	Print what function has done.

Details

It then returns a list of two vectors, containing the bad row & column indexes respectively.

Value

List (of two vectors: bad row & column indexes)

alexandruioanvoda/gwascelltyper documentation built on April 16, 2023, 8:03 p.m.