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)
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
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.