getSeqCMP: Get the subsequences from 2 allele types from the same HLA...

Description Usage Arguments Details Value Author(s) Examples

View source: R/HLAdbTools.R

Description

Extract from the HLAdb object, two sequences and the reference for a group of specific regions. The final sequences are the concatenation of the sequences of each region.

Usage

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getSeqCMP(HLAInfo, regionExt, typeS1, typeS2)

Arguments

HLAInfo

An object of class HLAdb containing information from HLA database.

regionExt

A data.frame containing 2 columns called Start and end. Those columns must contain integer entries corresponding to the regions to retain to create the subsequence. When more than one entry is present, the final subsequence will be the concatenation of all retained regions.

typeS1

A line of the tibble data from the object data return readHLADataset

typeS2

A line of the tibble data from the object data return readHLADataset HLA allele.

Details

TODO

Value

A list containing:

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

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library(dplyr)
## Get HLA protein database
data(hladb_protein_3.35.0)

## Two samples from same HLA gene
inputTibble <- tibble(SampleName=c("ERR188021", "ERR188021"),
                     AlleleName=c("1","2"),
                     GeneName=c("DRA", "DRA"),
                     AlleleGroup=c("01", "01"),
                     Protein=c("01", "01"),
                     SynSubst=c("01", "02"),
                     NonCoding=c("03", NA),
                     Suffix=c(NA, NA)
)
sample1 <- inputTibble[1,]
sample2 <- inputTibble[2,]#'
## Fix regions that will be extracted
regions <- data.frame(start=c(160, 200, 240), end=c(180, 220, 260))

## Extract subsequences
getSeqCMP(HLAInfo = hladb_protein_3.35.0, regionExt = regions,
    typeS1 = sample1, typeS2 = sample2)

NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq documentation built on Nov. 23, 2019, 1:57 a.m.