crunch {biovizBase} | R Documentation |
Fetching Granges from various data source, currently supported objects are TxDb, EnsDb, GAlignments and BamFile.
## S4 method for signature 'TxDb' crunch(obj, which, columns = c("tx_id", "tx_name","gene_id"), type = c("all", "reduce"), truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025) ## S4 method for signature 'EnsDb' crunch(obj, which, columns = c("tx_id", "gene_name","gene_id"), type = c("all", "reduce"), truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025) ## S4 method for signature 'GAlignments' crunch(obj, which, truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025) ## S4 method for signature 'BamFile' crunch(obj, which, ..., type = c("gapped.pair", "raw", "all"), truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025)
obj |
supported objects are |
which |
GRanges object. For TxDb object, could aslo be a list.
For |
columns |
columns to include in the output. |
type |
default 'all' is to show the full model, 'reduce' is to show a single model. |
truncate.gaps |
logical value, default |
truncate.fun |
shrinkage function. |
ratio |
numeric value, shrinking ratio. |
... |
arguments passed to function |
GRanges object.
Tengfei Yin
library(biovizBase) library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol, package = "biovizBase") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene obj <- txdb temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "all") temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "reduce") ## Fetching data from a EnsDb object. library(EnsDb.Hsapiens.v75) edb <- EnsDb.Hsapiens.v75 gr <- genesymbol["BRCA1"] seqlevels(gr) <- sub(seqlevels(gr), pattern="chr", replacement="") temp <- crunch(edb, which = gr) ## Alternatively, use the GenenameFilter from the AnnotationFilter package: temp <- crunch(edb, which = GenenameFilter("BRCA1")) ## Or a filter expression temp <- crunch(edb, which = ~ genename == "BRCA1")