samples {FRASER} | R Documentation |
samples
sets or gets the sample IDs; condition
;
nonSplicedReads
return a RangedSummarizedExperiment object
containing the counts for the non spliced reads overlapping splice
sites in the fds.
Getter/Setter methods for the FraserDataSet
The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object.
samples
sets or gets the sample IDs; condition
;
nonSplicedReads
return a RangedSummarizedExperiment object
containing the counts for the non spliced reads overlapping splice
sites in the fds.
Mapping of chromosome names
samples(object) samples(object) <- value condition(object) condition(object) <- value bamFile(object) bamFile(object) <- value name(object) name(object) <- value strandSpecific(object) strandSpecific(object) <- value pairedEnd(object) pairedEnd(object) <- value workingDir(object) workingDir(object) <- value scanBamParam(object) scanBamParam(object) <- value nonSplicedReads(object) nonSplicedReads(object) <- value ## S4 method for signature 'FraserDataSet' samples(object) ## S4 replacement method for signature 'FraserDataSet' samples(object) <- value ## S4 method for signature 'FraserDataSet' condition(object) ## S4 replacement method for signature 'FraserDataSet' condition(object) <- value ## S4 method for signature 'FraserDataSet' bamFile(object) ## S4 replacement method for signature 'FraserDataSet' bamFile(object) <- value ## S4 method for signature 'FraserDataSet' name(object) ## S4 replacement method for signature 'FraserDataSet' name(object) <- value ## S4 method for signature 'FraserDataSet' workingDir(object) ## S4 replacement method for signature 'FraserDataSet' workingDir(object) <- value ## S4 method for signature 'FraserDataSet' strandSpecific(object) ## S4 replacement method for signature 'FraserDataSet' strandSpecific(object) <- value ## S4 method for signature 'FraserDataSet' pairedEnd(object) ## S4 replacement method for signature 'FraserDataSet' pairedEnd(object) <- value ## S4 method for signature 'FraserDataSet' scanBamParam(object) ## S4 replacement method for signature 'FraserDataSet' scanBamParam(object) <- value ## S4 method for signature 'FraserDataSet' nonSplicedReads(object) ## S4 replacement method for signature 'FraserDataSet' nonSplicedReads(object) <- value FRASER.mcols.get(x, type = NULL, ...) FRASER.rowRanges.get(x, type = NULL, ...) mapSeqlevels(fds, style = "UCSC", ...)
object |
A FraserDataSet object. |
value |
The new value that should replace the current one. |
x |
A FraserDataSet object. |
type |
The psi type (psi3, psi5 or theta) |
... |
Further parameters. For mapSeqLevels: further parameters passed to GenomeInfoDb::mapSeqlevels(). |
fds |
FraserDataSet |
style |
The style of the chromosome names. |
Getter method return the respective current value.
Christian Mertes mertes@in.tum.de
Ines Scheller scheller@in.tum.de
fds <- createTestFraserDataSet() samples(fds) samples(fds) <- 1:dim(fds)[2] condition(fds) condition(fds) <- 1:dim(fds)[2] bamFile(fds) # file.paths or objects of class BamFile bamFile(fds) <- file.path("bamfiles", samples(fds), "rna-seq.bam") name(fds) name(fds) <- "My Analysis" workingDir(fds) workingDir(fds) <- tempdir() strandSpecific(fds) strandSpecific(fds) <- TRUE strandSpecific(fds) <- "reverse" strandSpecific(fds) scanBamParam(fds) scanBamParam(fds) <- ScanBamParam(mapqFilter=30) nonSplicedReads(fds) rowRanges(fds) rowRanges(fds, type="theta") mcols(fds, type="psi5") mcols(fds, type="theta") seqlevels(fds) seqlevels(mapSeqlevels(fds, style="UCSC")) seqlevels(mapSeqlevels(fds, style="Ensembl")) seqlevels(mapSeqlevels(fds, style="dbSNP"))