convert_counts: Perform a cpm/rpkm/whatever transformation of a count table.

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

Perform a cpm/rpkm/whatever transformation of a count table.

Description

I should probably tell it to also handle a simple df/vector/list of gene lengths, but I haven't. cp_seq_m is a cpm conversion of the data followed by a rp-ish conversion which normalizes by the number of the given oligo. By default this oligo is 'TA' because it was used for tnseq which should be normalized by the number of possible transposition sites by mariner. It could, however, be used to normalize by the number of methionines, for example – if one wanted to do such a thing.

Usage

convert_counts(count_table, method = "raw", ...)

Arguments

count_table	Matrix of count data.
method	Type of conversion to perform: edgecpm/cpm/rpkm/cp_seq_m.
...	Options I might pass from other functions are dropped into arglist, used by rpkm (gene lengths) and divide_seq (genome, pattern to match, and annotation type).

Value

Dataframe of cpm/rpkm/whatever(counts)

See Also

[edgeR] [Biobase]

Examples

## Not run: 
 converted_table = convert_counts(count_table, method='cbcbcpm')

## End(Not run)

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