Description Usage Arguments Value Author(s)
Retrieve a consensus set of ATAC peaks from the snakeATAC pipline run
1 2 3 4 5 6 7 8 9 10 11 12 13 | getPeakSet.snakeATAC(
sampleAnnot,
filePrefixCol,
genome,
dataDir,
sampleIdCol = filePrefixCol,
type = "summits_no_fw",
unifWidth = 500L,
replicateCol = NA,
replicatePercReq = 1,
replicateConsSelect = FALSE,
keepOvInfo = FALSE
)
|
sampleAnnot |
data.frame specifying the sample annotation table |
filePrefixCol |
column name specifying the file prefix for each sample in the sample annotation table |
genome |
genome assembly |
dataDir |
directory where the files are located |
sampleIdCol |
column name or index in the sample annotation table containing unique sample identifiers |
type |
input data type. Currently only "summits_no_fw" (non-overlapping, fixed-width peaks deduced from summits) |
unifWidth |
width of the peaks if the results have uniform peak lengths |
replicateCol |
column name specifying the replicate group for cross-checking coverage across replicates |
replicatePercReq |
percentile of replicates in a group required to contain a peak in order to keep it. E.g. a value of 1 (default) means that all replicates in a group are required to contain that peak in order to keep it. |
replicateConsSelect |
if set, the peak set will also be checked for consistency, i.e. in order to retain a peak
it has to be consistently be present or absent in each replicate group (as specified in |
keepOvInfo |
keep annotation columns in the elementMetadata of the results specifying whether a consensus peak overlaps with a peak in each sample |
GRanges
object containing consensus peak set
Fabian Mueller
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