readQueryFile {branchpointer} | R Documentation |
Reads and formats a manually generated query file, and finds realtive locations of the closest annotated exons Converts unstranded SNPs to two entries for each strand. Checks for duplicate names and replaces if found.
readQueryFile(queryFile, queryType, exons, maxDist = 50, filter = TRUE)
queryFile |
tab delimited file containing query information. For intronic regions should be in the format: region id, chromosome name, region start, region end, strand. For SNP variants should be in the format: SNP id, chromosome name, SNP position, strand, reference allele (A/T/C/G), alternative allele (A/T/C/G) |
queryType |
type of query file ( |
exons |
GRanges containing exon co-ordinates. Should be produced by gtfToExons() |
maxDist |
maximum distance a SNP can be from an annotated 3' exon. |
filter |
remove SNP queries prior to finding finding nearest exons. |
Formatted query GRanges
Beth Signal
smallExons <- system.file("extdata","gencode.v26.annotation.small.gtf", package = "branchpointer") exons <- gtfToExons(smallExons) querySNPFile <- system.file("extdata","SNP_example.txt", package = "branchpointer") querySNP <- readQueryFile(querySNPFile, queryType = "SNP", exons) queryIntronFile <- system.file("extdata","intron_example.txt", package = "branchpointer") queryIntron <- readQueryFile(queryIntronFile,queryType = "region", exons)