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

In NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq: HLA typing clustering and visualization based on specific similarity metrics

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

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:

• refSeq a character string containing the reference.

• seqS1 a character string containing the sequence of the first HLA allele.

• seqS2 a character string containing the sequence of the second HLA allele.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

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.