geneTrack.RdGenerate a track object from TxDb by given gene ids
geneTrack(ids, txdb, symbols, type = c("gene", "transcript"), asList = TRUE)Gene IDs. A vector of character. It should be keys in txdb.
An object of TxDb.
symbol of genes.
Output type of track, "gene" or "transcript".
Output a list of tracks or not. Default TRUE.
An object of track
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
ids <- c("3312", "390259", "341056", "79827")
symbols <- mget(ids, org.Hs.egSYMBOL)
geneTrack(ids, TxDb.Hsapiens.UCSC.hg19.knownGene, symbols)
#> $`3312`
#> This is an object of track
#> slot name: HSPA8
#> slot type: gene
#> slot format:
#> slot dat:
#> GRanges object with 23 ranges and 5 metadata columns:
#> seqnames ranges strand | feature id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> HSPA8 chr11 122928200-122928441 - | utr3 3312
#> HSPA8 chr11 122928442-122928536 - | CDS 3312
#> HSPA8 chr11 122928537-122928627 - | CDS 3312
#> HSPA8 chr11 122928960-122929192 - | CDS 3312
#> HSPA8 chr11 122929340-122929474 - | CDS 3312
#> ... ... ... ... . ... ...
#> HSPA8 chr11 122931301-122931506 - | CDS 3312
#> HSPA8 chr11 122931828-122932032 - | CDS 3312
#> HSPA8 chr11 122932033-122932037 - | utr5 3312
#> HSPA8 chr11 122932772-122932901 - | utr5 3312
#> HSPA8 chr11 122933055-122933186 - | utr5 3312
#> exon transcript gene
#> <character> <character> <character>
#> HSPA8 3312_1 unknown HSPA8
#> HSPA8 3312_1 unknown HSPA8
#> HSPA8 3312_2 unknown HSPA8
#> HSPA8 3312_3 unknown HSPA8
#> HSPA8 3312_4 unknown HSPA8
#> ... ... ... ...
#> HSPA8 3312_15 unknown HSPA8
#> HSPA8 3312_16 unknown HSPA8
#> HSPA8 3312_16 unknown HSPA8
#> HSPA8 3312_17 unknown HSPA8
#> HSPA8 3312_18 unknown HSPA8
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> slot dat2:
#> GRanges object with 0 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> -------
#> seqinfo: no sequences
#> slot style: try object$style to see details.
#>
#> $`341056`
#> This is an object of track
#> slot name: SAE1P1
#> slot type: gene
#> slot format:
#> slot dat:
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | feature
#> <Rle> <IRanges> <Rle> | <character>
#> SAE1P1 chr11 122888274-122890319 + | ncRNA
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> slot dat2:
#> GRanges object with 0 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> -------
#> seqinfo: no sequences
#> slot style: try object$style to see details.
#>
#> $`390259`
#> This is an object of track
#> slot name: BSX
#> slot type: gene
#> slot format:
#> slot dat:
#> GRanges object with 3 ranges and 5 metadata columns:
#> seqnames ranges strand | feature id exon
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> BSX chr11 122848357-122848599 - | CDS 390259 390259_1
#> BSX chr11 122849969-122850165 - | CDS 390259 390259_2
#> BSX chr11 122852118-122852379 - | CDS 390259 390259_3
#> transcript gene
#> <character> <character>
#> BSX unknown BSX
#> BSX unknown BSX
#> BSX unknown BSX
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> slot dat2:
#> GRanges object with 0 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> -------
#> seqinfo: no sequences
#> slot style: try object$style to see details.
#>
#> $`79827`
#> This is an object of track
#> slot name: CLMP
#> slot type: gene
#> slot format:
#> slot dat:
#> GRanges object with 9 ranges and 5 metadata columns:
#> seqnames ranges strand | feature id
#> <Rle> <IRanges> <Rle> | <character> <character>
#> CLMP chr11 122943033-122944181 - | utr3 79827
#> CLMP chr11 122944182-122944482 - | CDS 79827
#> CLMP chr11 122945410-122945551 - | CDS 79827
#> CLMP chr11 122953793-122953915 - | CDS 79827
#> CLMP chr11 122954388-122954555 - | CDS 79827
#> CLMP chr11 122955220-122955421 - | CDS 79827
#> CLMP chr11 122968503-122968660 - | CDS 79827
#> CLMP chr11 123065621-123065648 - | CDS 79827
#> CLMP chr11 123065649-123066007 - | utr5 79827
#> exon transcript gene
#> <character> <character> <character>
#> CLMP 79827_1 unknown CLMP
#> CLMP 79827_1 unknown CLMP
#> CLMP 79827_2 unknown CLMP
#> CLMP 79827_3 unknown CLMP
#> CLMP 79827_4 unknown CLMP
#> CLMP 79827_5 unknown CLMP
#> CLMP 79827_6 unknown CLMP
#> CLMP 79827_7 unknown CLMP
#> CLMP 79827_7 unknown CLMP
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#> slot dat2:
#> GRanges object with 0 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> -------
#> seqinfo: no sequences
#> slot style: try object$style to see details.
#>