Created
November 3, 2010 02:41
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library(Rsamtools) | |
library(ShortRead) | |
gene_locations <- read.csv("gene_locations.csv") | |
gr <- GRanges( seqnames = gene_locations$Scaffold_name, | |
ranges = IRanges(start=gene_locations$Gene.Start,end=gene_locations$Gene.Stop,names=gene_locations$locus_tag), | |
strand = gene_locations$Gene.Strand) | |
#> head(gene_locations) | |
# locus Gene.name locus_tag Locus_evidence_level Scaffold.Number Scaffold_name | |
#1 2 SNOG_00002 3 1 scaffold_1 | |
#2 3 SNOG_00003 2 1 scaffold_1 | |
#3 4 SNOG_00004 3 1 scaffold_1 | |
#4 5 SNOG_00005 3 1 scaffold_1 | |
#5 6 SNOG_00006 3 1 scaffold_1 | |
#6 7 SNOG_00007 3 1 scaffold_1 | |
# Gene.Start Gene.Stop Gene.Strand | |
#1 22020 24466 + | |
#2 25842 26135 + | |
#3 26209 29547 - | |
#4 30072 31598 + | |
#5 32042 33094 + | |
#6 33307 33642 - | |
#> gr | |
#GRanges with 100 ranges and 0 elementMetadata values | |
# seqnames ranges strand | | |
# <Rle> <IRanges> <Rle> | | |
#SNOG_00002 scaffold_1 [22020, 24466] + | | |
#SNOG_00004 scaffold_1 [26209, 29547] - | | |
#SNOG_00005 scaffold_1 [30072, 31598] + | | |
#SNOG_00006 scaffold_1 [32042, 33094] + | | |
#SNOG_00007 scaffold_1 [33307, 33642] - | | |
#SNOG_00008 scaffold_1 [33962, 34992] - | | |
#SNOG_00010 scaffold_1 [39124, 40913] - | | |
#SNOG_00011 scaffold_1 [41484, 43978] - | | |
#SNOG_00012 scaffold_1 [45102, 45308] + | | |
# ... ... ... ... ... | |
#SNOG_00120 scaffold_1 [308457, 309143] + | | |
#SNOG_00121 scaffold_1 [310554, 310751] - | | |
#SNOG_00122 scaffold_1 [310817, 312067] - | | |
#SNOG_00126 scaffold_1 [315859, 316811] - | | |
#SNOG_00127 scaffold_1 [318645, 319559] - | | |
#SNOG_00128 scaffold_1 [319911, 321243] + | | |
#SNOG_00129 scaffold_1 [321461, 323775] + | | |
#SNOG_00130 scaffold_1 [323824, 324134] + | | |
#SNOG_00131 scaffold_1 [324364, 325175] + | |
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