In ShihChingYu/MRAT: Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants

Install the package

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

Load the data for convet tanscript ID

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

Excute in convert_transcriptID()

new_dat<-convert_transcriptID(dat, db, dat_filter = "refseq_mrna")

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

ShihChingYu/MRAT documentation built on May 31, 2021, 12:58 p.m.