tr2g_EnsDb: Get transcript and gene info from EnsDb objects

In sarangian/RNASeqDEA: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

Description

Bioconductor provides Ensembl genome annotation in AnnotationHub; older versions of Ensembl annotation can be obtained from packages like EnsDb.Hsapiens.v86. This is an alternative to querying Ensembl with biomart; Ensembl's server seems to be less stable than that of Bioconductor. However, more information and species are available on Ensembl biomart than on AnnotationHub.

Usage

tr2g_EnsDb(ensdb, other_attrs = NULL, use_gene_name = TRUE,
  use_transcript_version = TRUE, use_gene_version = TRUE)

Arguments

ensdb	Ann EnsDb object, such as from AnnotationHub or EnsDb.Hsapiens.v86.
other_attrs	Character vector. Other attributes to get from the EnsDb object, such as gene symbol and position on the genome. Use columns to see which attributes are available.
use_gene_name	Logical, whether to get gene names.
use_transcript_version	Logical, whether to include version number in the Ensembl transcript ID. 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.
use_gene_version	Logical, whether to include version number in the Ensembl gene ID. Unlike transcript version number, it's up to you whether to include gene version number.

Value

A data frame with at least 2 columns: gene for gene ID, transcript for transcript ID, and optionally gene_name for gene names. If other_attrs has been specified, then those will also be columns in the data frame returned.

See Also

Other functions to retrieve transcript and gene info: sort_tr2g, tr2g_TxDb, tr2g_ensembl, tr2g_fasta, tr2g_gff3, tr2g_gtf, transcript2gene

Examples

library(EnsDb.Hsapiens.v86)
tr2g_EnsDb(EnsDb.Hsapiens.v86, use_transcript_version = FALSE,
  use_gene_version = FALSE)

sarangian/RNASeqDEA documentation built on Dec. 8, 2019, 5:24 p.m.