DBA object methods {DiffBind} | R Documentation |
Standard S3 methods for DBA object.
## S3 method for class 'DBA' print(x, ...) ## S3 method for class 'DBA' summary(object, ...) ## S3 method for class 'DBA' plot(x, ...)
x |
DBA object |
object |
DBA object |
... |
Arguments passed on to parent methods |
S3 methods for DBA object from the DiffBind
package.
DBA objects are usually constructed using the dba
function.
There are a number of internal parameters that can be set,
and defaults overridden, by setting DBA$config
options:
DBA$config$AnalysisMethod:
either DBA_DESEQ2
or DBA_EDGER
.
DBA$config$th:
default threshold for reporting and plotting analysis results.
DBA$config$DataType:
default class for peaks and reports
(DBA_DATA_GRANGES, DBA_DATA_RANGEDDATA, or DBA_DATA_FRAME
).
DBA$config$RunParallel:
logical indicating if counting and analysis
operations should be run in parallel using multicore by default.
DBA$config$cores:
number of cores to use when performing multi-core parallel processing.
DBA$config$minQCth:
numeric, for filtering reads based on mapping
quality score; only reads with a mapping quality score
greater than or equal to this will be counted.
DBA$config$fragmentSize:
numeric indicating mean fragment size for single-end counting.
Reads will be extended to this length before counting overlaps.
May be a vector of lengths, one for each sample.
DBA$config$bCorPlot:
logical indicating that a correlation heatmap
should be plotted automatically
DBA$config$ReportInit:
string to append to the beginning of saved report file names.
DBA$config$bUsePval:
logical, default indicating whether to use FDR
(FALSE
) or p-values (TRUE
).
DBA$config$doBlacklist:
logical, whether to attempt to find and apply
a blacklist if none is present when running dba.analyze
.
DBA$config$doGreylist
logical, whether to attempt to generate and apply
a greylist if none is present when running dba.analyze
.
DBA$config$DataType
The class of object for returned reports and peaksets:
DBA$config$mergeOverlap:
The overlap (in basepairs) between peaks to merge when generating
a consensus peakset.
A positive valuecontrols how many basepairs peaks
must overlap to be merged,
while a negative value will result in non-overlapping peaks to be merged,
If absent, the default value of 1
will result in any peaks
overlapping by at least one basepair to be merged into a single interval.
DBA$config$design:
When calling dba.contrast
, if design
parameter is
missing, this will be used as the value for that parameter.
DBA$config$edgeR$bTagwise:
logical
indicating if edgeR::estimateGLMTagwiseDisp
should
be called when performing an edgeR
analysis.
If absent the default is TRUE
, so setting this to FALSE
prevents the tagwise dispersion estimate form being calculated.
DBA$config$DESeq2$fitType:
logical
indicating the fitType
to be used in DESeq2::estimateDispersions
when performing a DESeq2
analysis.
If absent the default is local
.
DBA$config$savePrefix:
When calling dba.save
or dba.load
,
this value (if present)
will override the default value for the pre
parameter.
DBA$config$saveExt:
When calling dba.save
or dba.load
,
this value (if present)
will override the default value for the ext
parameter.
DBA$config$greylist.pval:
pvalue cutoff to use when generating a greylist
using GreyListChIP::calcThreshold
.
If missing, the default is 0.999
DBA$config$saveExt:
When calling dba.save
, this value (if present)
will override the default value for the ext
parameter.
DBA$config$yieldSize:
yieldSize indicating how many reads to process at one time; default is 5000000.
The lower this value, the less memory will be used, but the more time it will take to
complete the count operation.
DBA$config$intersectMode:
mode indicating which overlap algorithm to use;
default is "IntersectionNotEmpty"
DBA$config$singleEnd:
logical
indicating if reads are single end;
if NULL
, status will be automatically detected.
DBA$config$fragments:
logical
indicating how unmatched reads are counted;
default is FALSE
.
DBA$config$scanbamparam:
ScanBamParam
object to pass to summarizeOverlaps
.
If present, bRemoveDuplicates
is ignored.
DBA$config$pp.style:
Sets style
parameter for profileplyr::BamBigwig_to_chipProfile
when calling dba.plotProfile.
DBA$config$pp.nOfWindows:
Sets nOfWindow
parameter for
profileplyr::BamBigwig_to_chipProfile
when calling dba.plotProfile.
DBA$config$bin_size:
Sets bin_size
parameter for
profileplyr::BamBigwig_to_chipProfile
when calling dba.plotProfile.
DBA$config$distanceAround:
Sets distanceAround
parameter for
profileplyr::BamBigwig_to_chipProfile
when calling dba.plotProfile.
DBA$config$distanceUp:
Sets distanceUp
parameter for
profileplyr::BamBigwig_to_chipProfile
when calling dba.plotProfile.
DBA$config$distanceDown:
Sets distanceDown
parameter for
profileplyr::BamBigwig_to_chipProfile
when calling dba.plotProfile.
DBA$config$id:
character
string to use to replace "ID"
when displaying a DBA
object (dba.show
)
DBA$config$group:
character
string to use to replace "Group"
when displaying a DBA
object (dba.show
)
DBA$config$tissue:
character
string to use to replace "Tissue"
when displaying a DBA
object (dba.show
)
DBA$config$factor:
character
string to use to replace "Factor"
when displaying a DBA
object (dba.show
)
DBA$config$condition:
character
string to use to replace "Condition"
when displaying a DBA
object (dba.show
)
DBA$config$treatment:
character
string to use to replace "Treatment"
when displaying a DBA
object (dba.show
)
DBA$config$replicate:
character
string to use to replace "Replicate"
when displaying a DBA
object (dba.show
)
DBA$config$caller:
character
string to use to replace "Caller"
when displaying a DBA
object (dba.show
)
DBA$config$reads:
character
string to use to replace "Reads"
when displaying a DBA
object (dba.show
)
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