SeqAnnotate: SeqAnnotate

In brengong/ConservationtextmineR:

Description

Requires a data table containing a column labeled "ensembl_peptide_id" or "ensembl_transcript_id" Returns a data.table contaiining "ensembl_peptide_id", "external_gene_name", "transcription_start_site", "transcript_start", "transcript_end", "chromosome_name" for all species compiled

Usage

SeqAnnotate(DT, type)

Arguments

DT	a data table containing a column labeled "ensembl_peptide_id" or "ensembl_transcript_id"
type	single character string either "protein" or "mRNA". If "protein", requires the "ensembl_peptide_id" column and returns a data table containing protein ensembl peptide id's. If "mRNA", requires the "ensembl_transcript_id" column and returns a data table containing protein ensembl transcript id's.

Value

A data.table contaiining "ensembl_peptide_id"/"ensembl_transcript_id", "external_gene_name", "transcription_start_site", "transcript_start", "transcript_end", "chromosome_name" for all species compiled

Author(s)

Brendan Gongol

Examples

library(data.table)
setwd("C:/Users/Brendan/Dropbox/Brendan Documents/R programming/bioinformatics/proteomes/2016-4-29 Proteomes")
Proteome <- fread("species protein compilation.xls")
head(SeqAnnotate(DT = Proteome, type = "protein"))

library(data.table)
setwd("C:/Users/Brendan/Dropbox/Brendan Documents/R programming/bioinformatics/cDNA_transcriptome/2016-3-6 cDNA transcriptomes")
Transcriptome <- fread("species mRNA compilation.xls")
head(SeqAnnotate(Transcriptome, type = "mRNA"))

brengong/ConservationtextmineR documentation built on July 29, 2019, 10:05 a.m.