write_velocity_output: Write the files for RNA velocity to disk

Description Usage Arguments Value

View source: R/velocity.R

Description

Write the files for RNA velocity to disk, in the specified output directory.

Usage

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write_velocity_output(
  out_path,
  introns,
  Genome,
  Transcriptome,
  isoform_action,
  exon_option,
  tr2g_cdna,
  compress_fa,
  width
)

Arguments

out_path

Directory to save the outputs written to disk. If this directory does not exist, then it will be created.

introns

Intronic ranges plus flanking region, returned by get_intron_flanks.

Genome

Either a BSgenome or a XStringSet object of genomic sequences, where the intronic sequences will be extracted from. Use genomeStyles to check which styles are supported for your organism of interest; supported styles can be interconverted. If the style in your genome or annotation is not supported, then the style of chromosome names in the genome and annotation should be manually set to be consistent.

Transcriptome

A XStringSet, a path to a fasta file (can be gzipped) of the transcriptome which contains sequences of spliced transcripts, or NULL. The transcriptome here will be concatenated with the intronic sequences to give one fasta file. When NULL, the transriptome sequences will be extracted from the genome given the gene annotation, so it will be guaranteed that transcript IDs in the transcriptome and in the annotation match. Otherwise, the type of transcript ID in the transcriptome must match that in the gene annotation supplied via argument X.

isoform_action

Character, indicating action to take with different transcripts of the same gene. Must be one of the following:

collapse

First, the union of all exons of different transcripts of a gene will be taken. Then the introns will be inferred from this union. Only the flanked intronic sequences are affected; isoforms will always be taken into account for spliced sequences or exon-exon junctions.

separate

Introns from different transcripts will be kept separate.

exon_option

Character, indicating how exonic sequences should be included in the kallisto index. Must be one of the following:

full

The full cDNA sequences, which include the full exonic sequences, will be used. This is the default.

junction

Only the exon-exon junctions, with L-1 bases on each side of the junctions, will be used.

tr2g_cdna

A data frame with columns transcript and gene that maps transcripts to genes for spliced transcripts.

compress_fa

Logical, whether to compress the output fasta file. If TRUE, then the fasta file will be gzipped.

width

Maximum number of letters per line of sequence in the output fasta file. Must be an integer.

Value

Nothing into the R session. The files are written to disk.


lambdamoses/BUStoolsR documentation built on June 9, 2021, 6:15 p.m.