VariantSort: VariantSort

In brengong/ConservationtextmineR:

Description

Takes a Data.table containing a compilation of mRNA or protein sequences from a variety of species and either returns a data table containing the longest transcript identified for each protein and species or each variant labeled according to the length of the sequence. The data.table requires a column labeled "Scientific_Name", a column labeled "Sequence", and a column labeled "external_gene_name".

Usage

VariantSort(DT, variant)

Arguments

DT	a data table with three columns labeled Sequence, Scientific_Name, external_gene_name
variant	a character statement either "MAX", "ALL", or "MIN". If "MAX", returns a data table containing the longest sequence for each sequence and species. If "ALL", returns a data table containing each variant labeled according to the length of the sequence. If "MIN", returns a data table containing the shortest sequence for each sequence and species.

Value

A data table containing the longest transcripts for each protein and species or each variant labeled according to the length of the sequence.

Author(s)

Brendan Gongol

Examples

 setwd("C:/Users/Brendan/Desktop/oxidative stress surfactant bioinformatics")
Surfactant_Transcripts <- fread("1 Surfactant Transcripts.xls")
SURF_HUM <- Surfactant_Transcripts[Surfactant_Transcripts$Common_Name == "Human",]
sor <- VariantSort(SURF_HUM, variant = "MAX")
sor[,c(1, 5:11), with = FALSE]
sor <- VariantSort(SURF_HUM, variant = "ALL")
sor[,c(1, 5:12), with = FALSE]
sor <- VariantSort(SURF_HUM, variant = "MIN")
sor[,c(1, 5:11), with = FALSE]

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