normalize_collection: Normalize collection table

In Miswi/RiboCrypt: Interactive visualization in genomics

Normalize collection table

Description

Normalize collection table

Usage

normalize_collection(
  table,
  normalization,
  lib_sizes = NULL,
  kmer = 1L,
  add_logscore = TRUE,
  split_by_frame = FALSE
)

Arguments

table	a data.table in long format
normalization	a character string, which mode, for options see RiboCrypt:::normalizations
lib_sizes	named integer vector, default NULL. If given will do a pre tpm normalization for full library sizes
kmer	integer, default 1L (off), if > 1 will smooth out signal with sliding window size kmer.
add_logscore	logical, default TRUE, adds a log(score + 1) to table
split_by_frame	logical, default FALSE For kmer sliding window, should it split by frame

Value

a data.table of normalized results

Miswi/RiboCrypt documentation built on April 16, 2024, 10:47 a.m.