filter_counts: Call various count filters.

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

Call various count filters.

Description

This calls the various filtering functions in genefilter along with suggestions made in our lab meetings; defaulting to the threshold based filter suggested by Hector.

Usage

filter_counts(
  count_table,
  method = "cbcb",
  p = 0.01,
  A = 1,
  k = 1,
  cv_min = 0.01,
  cv_max = 1000,
  thresh = 2,
  min_samples = 2,
  ...
)

Arguments

count_table	Some counts to filter.
method	Filtering method to apply (cbcb, pofa, kofa, cv right now).
p	Used by genefilter's pofa().
A	Also for pofa().
k	Used by genefilter's kofa().
cv_min	Used by genefilter's cv().
cv_max	Also used by cv().
thresh	Minimum threshold across samples for cbcb.
min_samples	Minimum number of samples for cbcb.
...	More options might be needed, especially if I fold cv/p/etc into ...

Value

Data frame of filtered counts.

See Also

[genefilter]

Examples

## Not run: 
 new <- filter_counts(old)

## End(Not run)

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