dot-get_velocity_files: Generate RNA velocity files for GRanges

Description Usage Arguments Value

Description

Generate RNA velocity files for GRanges

Usage

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.get_velocity_files(
  gr,
  L,
  Genome,
  Transcriptome = NULL,
  out_path = ".",
  style = c("genome", "Ensembl", "UCSC", "NCBI", "other"),
  isoform_action = c("separate", "collapse"),
  exon_option = c("full", "junction"),
  transcript_id = "transcript_id",
  gene_id = "gene_id",
  transcript_version = "transcript_version",
  gene_version = "gene_version",
  version_sep = ".",
  transcript_biotype_col = "transcript_biotype",
  gene_biotype_col = "gene_biotype",
  transcript_biotype_use = "all",
  gene_biotype_use = "all",
  chrs_only = TRUE,
  save_filtered_gtf = FALSE,
  compress_fa = FALSE,
  width = 80L
)

Arguments

gr

A GRanges object for gene annotation.

L

Length of the biological read. For instance, 10xv1: 98 nt, 10xv2: 98 nt, 10xv3: 91 nt, Drop-seq: 50 nt. If in doubt check read length in a fastq file for biological reads with the bash commands: If the fastq file is gzipped, then do zcat your_file.fastq.gz | head on Linux. If on Mac, then zcat < your_file.fastq.gz | head. Then you will see lines with nucleotide bases. Copy one of those lines and determine its length with str_length in R or echo -n <the sequence> | wc -c in bash. Which file corresponds to biological reads depends on the particular technology.

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.

out_path

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

style

Formatting of chromosome names. Use genomeStyles to check which styles are supported for your organism of interest and what those styles look like. This can also be a style supported for your organism different from the style used by the annotation and the genome. Then this style will be used for both the annotation and the genome. Can take the following values:

genome

If style of the annnotation is different from that of the genome, then the style of the genome will be used.

other

Custom style, need to manually ensure that the style in annotation matches that of the genome.

Ensembl

Or UCSC or NCBI, whichever is supported by your species of interest.

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.

transcript_id

Character vector of length 1. Tag in attribute field corresponding to transcript IDs. This argument must be supplied and cannot be NA or NULL. Will throw error if tag indicated in this argument does not exist.

gene_id

Character vector of length 1. Tag in attribute field corresponding to gene IDs. This argument must be supplied and cannot be NA or NULL. Note that this is different from gene symbols, which do not have to be unique. This can be Ensembl or Entrez IDs. However, if the gene symbols are in fact unique for each gene, you may supply the tag for human readable gene symbols to this argument. Will throw error if tag indicated in this argument does not exist. This is typically "gene_id" for annotations from Ensembl and "gene" for refseq.

transcript_version

Character vector of length 1. Tag in attribute field corresponding to transcript version number. If your GTF file does not include transcript version numbers, or if you do not wish to include the version number, then use NULL for this argument. To decide whether to include transcript version number, check whether version numbers are included in the transcripts.txt in the kallisto output directory. If that file includes version numbers, then trannscript version numbers must be included here as well. If that file does not include version numbers, then transcript version numbers must not be included here.

gene_version

Character vector of length 1. Tag in attribute field corresponding to gene version number. If your GTF file does not include gene version numbers, or if you do not wish to include the version number, then use NULL for this argument. Unlike transcript version number, it's up to you whether to include gene version number.

version_sep

Character to separate bewteen the main ID and the version number. Defaults to ".", as in Ensembl.

transcript_biotype_col

Character vector of length 1. Tag in attribute field corresponding to transcript biotype.

gene_biotype_col

Character vector of length 1. Tag in attribute field corresponding to gene biotype.

transcript_biotype_use

Character, can be "all" or a vector of transcript biotypes to be used. Transcript biotypes aren't entirely the same as gene biotypes. For instance, in Ensembl annotation, retained_intron is a transcript biotype, but not a gene biotype. If "cellranger", then a warning will be given. See data("ensembl_tx_biotypes") for all available transcript biotypes from Ensembl.

gene_biotype_use

Character, can be "all", "cellranger", or a vector of gene biotypes to be used. If "cellranger", then the biotypes used by Cell Ranger's reference are used. See data("cellranger_biotypes") for gene biotypes the Cell Ranger reference uses. See data("ensembl_gene_biotypes") for all available gene biotypes from Ensembl. Note that gene biotypes and transcript biotypes are not always the same.

chrs_only

Logical, whether to include chromosomes only, for GTF and GFF files can contain annotations for scaffolds, which are not incorporated into chromosomes. This will also exclude haplotypes. Defaults to TRUE. Only applicable to species found in genomeStyles().

save_filtered_gtf

Logical. If filtering type, biotypes, and/or chromosomes, whether to save the filtered GRanges as a GTF file.

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

See get_velocity_files


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