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I have granges (feat_ranges) i want to find index of row corresponding to a gene in this range. Example given below
library(GenomicFeatures) library("biomaRt") library(GenomeInfoDb) txdb <- makeTxDbFromBiomart(biomart = "ensembl", dataset = "scerevisiae_gene_ensembl") myfeatures <- c("tx_type", "promoter", "intron", "exon", "cds", "intergenic") feat_ranges <- genFeatures(txdb, featuretype=myfeatures, reduce_ranges=FALSE, upstream=1000, downstream=0)
I want to find index row corresponding to "YAL066W" (feature_by metadata column) as value 4.
thanks
> feat_ranges GRangesList object of length 12: $protein_coding GRanges object with 6692 ranges and 3 metadata columns: seqnames ranges strand | feature_by featuretype_id featuretype <Rle> <IRanges> <Rle> | <CharacterList> <character> <character> 1 [ 335, 649] + | YAL069W YAL069W protein_coding 1 [ 538, 792] + | YAL068W-A YAL068W-A protein_coding 1 [ 2480, 2707] + | YAL067W-A YAL067W-A protein_coding 1 [10091, 10399] + | YAL066W YAL066W protein_coding 1 [12046, 12426] + | YAL064W-B YAL064W-B protein_coding ... ... ... ... ... ... ... ... 17 [65770, 66174] + | Q0182 Q0182 protein_coding 17 [73758, 74513] + | Q0250 Q0250 protein_coding 17 [74495, 75984] + | Q0255 Q0255 protein_coding 17 [79213, 80022] + | Q0275 Q0275 protein_coding 17 [85554, 85709] + | Q0297 Q0297 protein_coding ... <11 more elements> ------- seqinfo: 17 sequences (1 circular) from an unspecified genome