semantic_expt_filter: Remove/keep specifically named genes from an expt.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Remove/keep specifically named genes from an expt.

Description

I find subsetting weirdly confusing. Hopefully this function will allow one to include/exclude specific genes/families based on string comparisons.

Usage

semantic_expt_filter(
  input,
  invert = FALSE,
  topn = NULL,
  semantic = c("mucin", "sialidase", "RHS", "MASP", "DGF", "GP63"),
  semantic_column = "description"
)

Arguments

input	Expt to filter.
invert	The default is to remove the genes with the semantic strings. Keep them when inverted.
topn	Take the topn most abundant genes rather than a text based heuristic.
semantic	Character list of strings to search for in the annotation data.
semantic_column	Column in the annotations to search.

Value

A presumably smaller expt.

See Also

[Biobase]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.