denest_sleuth_boots: Extract bootstrap counts into a less nested structure.

In bartongroup/RATS: Relative Abundance of Transcripts

Extract bootstrap counts into a less nested structure.

Description

*Legacy function*

Usage

denest_sleuth_boots(
  slo,
  annot,
  samples,
  COUNTS_COL = "tpm",
  BS_TARGET_COL = "target_id",
  TARGET_COL = "target_id",
  PARENT_COL = "parent_id",
  threads = 1
)

Arguments

slo	A sleuth object.
annot	A data.frame matching transcript identfier to gene identifiers.
samples	A numeric vector of samples to extract counts for.
COUNTS_COL	The name of the column with the counts. (Default "tpm")
BS_TARGET_COL	The name of the column with the transcript IDs. (Default "target_id")
TARGET_COL	The name of the column for the transcript identifiers in annot. (Default "target_id")
PARENT_COL	The name of the column for the gene identifiers in annot. (Default "parent_id")
threads	Number of threads. (Default 1)

Details

It extracts the bootstrap data from the older-style sleuth object. As of sleuth version 0.29, the bootstrap data is no longer kept in the object.

Value

A list of data.tables, one per sample, containing all the bootstrap counts of the smaple. First column contains the transcript IDs.

NA replaced with 0.

Transcripts in slo that are missing from annot will be skipped completely. Transcripts in annot that are missing from slo are automatically padded with NA, which we re-assign as 0.

bartongroup/RATS documentation built on June 8, 2022, 12:40 a.m.