SpeciesTFCons: SpeciesTFCons

In brengong/ConservationtextmineR:

Description

Takes a data.table containing the following columns: "Species", "gene_symbol", "Targeting_Factor" returns the data.table containing only Target names that are conserved between specified species for the original data.table (may contain additional species if they were in the original data.table but will only contain those promoters that are conserved between the specified species. It also may do the same thing for Targeting_Factor Target associations across species specified.

Usage

SpeciesTFCons(DT, Spec, provide)

Arguments

DT	the data table to query
Spec	a character vector containing the species to query.
provide	Target, TF_Target. If "Target", returns conserved Targets, If "TF_Target", returns only columns with Targeting_Factors that are paired with a Target for specified Species. It also returns an additional column with the paired Targeting_Factor and Target pair.

Value

The sequences in a string format that can be added to a data.table

Author(s)

Brendan Gongol

Examples

setwd("C:/Users/Brendan/Desktop/oxidative stress surfactant bioinformatics")
library(data.table)
DT25 <- fread("Raw Transcription factor hits.xls")
DT25 <- DT25[,c(1:6, 9:10), with = FALSE]
setnames(DT25, c("Consensus_Sequence", "start", "end", "Number_Hits", "TX_Factor", "MotifMap Degenerate consensus sequence", "promoter_name", "Species"),
         c("Consensus_Sequence", "start", "end", "Number_Hits", "Targeting_Factor", "MotifMap Degenerate consensus sequence", "gene_symbol", "Species"))
SP_MIN <- c("Human", "Mouse", "Rat")
SpeciesTFCons(DT = DT25,Spec = SP_MIN, provide = "Target" )
SpeciesTFCons(DT = DT25,Spec = SP_MIN, provide = "TF_Target" )

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