write_velocity_output: Write the files for RNA velocity to disk
In lambdamoses/BUStoolsR: kallisto | bustools R utilities

write_velocity_output

R Documentation

Write the files for RNA velocity to disk

Description

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

Usage

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.