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TransAT

TransAT is a package within the R programming language for converting RefSeq ID to Ensembl ID and mapping the genomic position, followed by providing variant allele frequencies and gene annotations.

Install the package

devtools::install_github("ShihChingYu/TransAT", force=T)
library(TransAT)

Usage of convet_tanscriptID()

Load the data for convet_tanscriptID()

  • load .csv of refseq ID
dat<-read.csv(system.file("extdata", "convertID_refseq_data.csv", package = "TransAT"),
              stringsAsFactors = FALSE, encoding = "UTF-8", row.names = NULL, sep = ",")
dat
  • load .csv of UCSC ID
dat_ucsc<-read.csv(system.file("extdata", "convertID_ucsc_data.csv", package = "TransAT"),
              stringsAsFactors = FALSE, encoding = "UTF-8", row.names = NULL, sep = ",")
dat_ucsc
  • load .bed of refseq ID
dat_b<-read.table(system.file("extdata", "convertID_refseq_data2.bed", package = "TransAT"),
              stringsAsFactors = FALSE, encoding = "UTF-8", row.names = NULL, sep = "\t", header=T)
dat_b

Excute in convert_transcriptID()

  • convert transcript refseq ID
new_dat<-convert_transcriptID(dat, db, dat_filter = "refseq_mrna")
  • convert transcript ucsc ID
new_dat_ucsc<-convert_transcriptID(dat_ucsc, db, dat_filter = "ucsc")

Result from the convert_transcriptID()

data(convertID_result, package = "TransAT")
convertID_result

Usage of pop_freq()

Load the data for getting population allele frequency

anno_freq_data<-read.csv(system.file("extdata",
                          "anno_freq_data.csv",
                          package = "TransAT"),
              stringsAsFactors = FALSE, encoding = "UTF-8", row.names = NULL, sep = ",")
anno_freq_data

Excute in pop_freq()

pop_dat<-pop_freq(anno_freq_data, pop="db_gnomAD_exome_freq")

Result from the pop_freq()

data(pop_result, package = "TransAT")
pop_result

This is the PDF depicting MAF of each global population with barplots.