compute_collection_table: Get collection table normalized in wide format

In Miswi/RiboCrypt: Interactive visualization in genomics

Get collection table normalized in wide format

Description

Get collection table normalized in wide format

Usage

compute_collection_table(
  path,
  lib_sizes,
  df,
  metadata_field,
  normalization,
  kmer,
  metadata,
  min_count = 0,
  format = "wide",
  value.var = "logscore",
  as_list = FALSE,
  subset = NULL,
  group_on_tx_tpm = NULL,
  split_by_frame = FALSE,
  ratio_interval = NULL
)

Arguments

path	the path to gene counts
lib_sizes	named integer vector, default NULL. If given will do a pre tpm normalization for full library sizes
df	the ORFik experiment to load the precomputed collection from. It must also have defined runIDs() for all samples.
metadata_field	the column name in metadata, to select to group on.
normalization	a character string, which mode, for options see RiboCrypt:::normalizations
kmer	integer, default 1L (off), if > 1 will smooth out signal with sliding window size kmer.
metadata	a data.table of metadata, must contain the Run column to select libraries.
min_count	integer, default 0. Minimum counts of coverage over transcript to be included.
format	character, default "wide", alternative "long". The format of the table output.
value.var	which column to use as scores, default "logscore"
as_list	logical, default FALSE. Return as list of size 2, count data.table and metadata data.table Set to TRUE if you need metadata subset (needed if you subset the table, to get correct matching)
split_by_frame	logical, default FALSE For kmer sliding window, should it split by frame

Value

a data.table in long or wide (default) format, if as list, it is a list of size 2 (see argument as_list)

Miswi/RiboCrypt documentation built on Nov. 9, 2024, 2:16 p.m.