Arguments
obj
An object derived from class RNAseq
chr.map
A data.frame describing the mapping of original chromosome
names towards wished chromosome names. See the details in
easyRNASeq. chr.sel
A vector of chromosome names to subset the final results.
cList
list of lists that contain count results
count
The feature used to summarize the reads. One of
'exons','features','genes','islands' or 'transcripts'.
filename
The full path of the file to use
filter
The filter to be applied when loading the data using the
"aln" format
format
The format of the reads, one of "aln","bam". If not "bam",
all the types supported by the ShortRead package are supported too.
As of version 1.3.5, it defaults to bam. gapped
Is the bam file provided containing gapped alignments?
min.cov
When computing read islands, the minimal coverage to take
into account for calling an island
min.length
The minimal size an island should have to be kept
max.gap
When computing read islands, the maximal gap size allowed
between two islands to merge them
plot
Whether or not to plot assessment graphs.
rnaSeq
An object derived from class RNAseq
summarization
A character defining which method to use when
summarizing reads by genes. So far, only "geneModels" is available.
silent
set to TRUE if you do not want messages to be printed out.
subType
character string defining a sub type of counts, i.e. for the
gene type one of bestExon or geneModel
type
- .extendCountList: character string specifying the type of count ("exons",
"transcripts", "genes" or islands)
- .doCount: the type of data when using the "aln" format. See the ShortRead
library.
validity.check
Shall UCSC chromosome name convention be enforced?
This is only supported for a set of organisms, which are
Dmelanogaster, Hsapiens, Mmusculus and Rnorvegicus;
otherwise the argument 'chr.map' can be used to complement it.
values
a named vector containing count results
...
additional arguments. See the details in
easyRNASeq.