mergeKallisto: Merge multiple Kallisto results, yielding a...

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

If no transcriptomes are specified (or the ones specified are not found), the resulting KallistoExperiment will have a rowData/rowRanges object which consists entirely of unannotated transcripts from chromosome "Unknown". If transcriptomes are specified and annotations for those transcriptomes are found, the transcripts described in the annotations will be fully annotated for transcript ID, gene ID, gene name, entrez ID, and transcript biotype, provided that these fields are supported in the annotation resources.

Usage

mergeKallisto(outputDirs = NULL, outputPath = ".", covariates = NULL,
  annotate = FALSE, collapse = "_mergedWith_", transcriptomes = NULL,
  parallel = TRUE, summarize = FALSE, ...)

Arguments

outputDirs	character: directories holding Kallisto results (NULL)
outputPath	character: base path to the outputDirs (default is .)
covariates	data.frame or DataFrame: per-sample covariates (NULL)
annotate	boolean: auto-annotate the transcripts? (FALSE)
collapse	string: collapsing string for indices ("_mergedWith_")
transcriptomes	string: collapsing string for indices ("_mergedWith_")
parallel	boolean: try to run the merge in parallel? (TRUE)
summarize	boolean: summarize bootstraps if found? (FALSE)
...	further arguments for KallistoExperiment constructor

Details

FIXME: automatically determine which transcriptomes were used (in process!)

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.