Object that holds allele counts, genomic positions and map-bias for a set of
SNPs
Usage
alleleCounts(x, strand = "*", return.class = "list")
## S4 method for signature 'ASEset'
alleleCounts(x, strand = "*", return.class = "list")
alleleCounts(x, ...) <- value
## S4 replacement method for signature 'ASEset'
alleleCounts(x, strand = "*", return.class = "array",
...) <- value
mapBias(x, ...)
## S4 method for signature 'ASEset'
mapBias(x, return.class = "list")
fraction(x, ...)
## S4 method for signature 'ASEset'
fraction(x, strand = "*",
top.fraction.criteria = "maxcount", verbose = FALSE, ...)
arank(x, return.type = "names", return.class = "list", strand = "*", ...)
frequency(x, ...)
genotype(x, ...)
## S4 method for signature 'ASEset'
genotype(x, return.class = "matrix")
genotype(x) <- value
## S4 replacement method for signature 'ASEset'
genotype(x) <- value
countsPerSnp(x, ...)
## S4 method for signature 'ASEset'
countsPerSnp(x, return.class = "matrix",
return.type = "mean", strand = "*")
countsPerSample(x, ...)
## S4 method for signature 'ASEset'
countsPerSample(x, return.class = "matrix",
return.type = "mean", strand = "*")
phase(x, ...)
## S4 method for signature 'ASEset'
phase(x, return.class = "matrix")
phase(x) <- value
## S4 replacement method for signature 'ASEset'
phase(x) <- value
mapBias(x) <- value
## S4 replacement method for signature 'ASEset'
mapBias(x) <- value
refExist(x)
## S4 method for signature 'ASEset'
refExist(x)
ref(x)
## S4 method for signature 'ASEset'
ref(x)
ref(x) <- value
## S4 replacement method for signature 'ASEset,ANY'
ref(x) <- value
altExist(x)
## S4 method for signature 'ASEset'
altExist(x)
alt(x)
## S4 method for signature 'ASEset'
alt(x)
alt(x) <- value
## S4 replacement method for signature 'ASEset,ANY'
alt(x) <- value
aquals(x, ...)
## S4 method for signature 'ASEset'
aquals(x)
aquals(x) <- value
## S4 replacement method for signature 'ASEset'
aquals(x) <- value
maternalAllele(x, ...)
## S4 method for signature 'ASEset'
maternalAllele(x)
paternalAllele(x, ...)
## S4 method for signature 'ASEset'
paternalAllele(x)
Arguments
x
ASEset object
strand
which strand of '+', '-' or '*'
return.class
return 'list' or 'array'
...
additional arguments
value
replacement variable
top.fraction.criteria
'maxcount', 'ref' or 'phase'
verbose
makes function more talkative
return.type
return 'names', rank or 'counts'
Details
An ASEset object differs from a regular RangedSummarizedExperiment object
in that the assays contains an array instead of matrix. This array has
ranges on the rows, sampleNames on the columns and variants in the third
dimension.
It is possible to use the commands barplot and locationplot on an ASEset
object see more details in barplot and
locationplot.
Three different alleleCount options are available. The simples one is the
* option, and is for experiments where the strand information is not
known e.g. non-stranded data. The unknown strand could also be for strand
specific data when the aligner could not find
any strand associated with the read, but this should normally not happen,
and if it does probably having an extremely low mapping quality.
Then there are an option too add plus
and minus stranded data. When using this, it is essential to make sure that
the RNA-seq experiment under analysis has in fact been created so that
correct strand information was obtained. The most functions will by default
have their strand argument set to '*'.
The phase information is stored by the convention of
'maternal chromosome|paternal chromosome', with 0 as reference allele and 1
as alternative allele. '|' when the phase is known and '/' when the phase is
unknown. Internally the information will be stored as an three dimensional
array, dim 1 for SNPs, dim 2 for Samples and dim 3 which is fixed and stores
maternal chromosome, paternal chromosome and phased (1 equals TRUE).
Value
An object of class ASEset containing location information and allele
counts for a number of SNPs measured in a number of samples on various
strand, as well as mapBias information. All data is stored in a manner
similar to the RangedSummarizedExperiment
class.
Table
table(...)
Arguments:
...
An ASEset object that contains the
variants of interest
The generics for table does not easily allow more than one argument
so in respect to the different strand options, table will
return a SimpleList with length 3, one element for each strand.