BSFDataSet {BindingSiteFinder} | R Documentation |
BSFDataSet
contains the class GenomicRanges
, which is used to
store input ranges. Alongside with the iCLIP signal in list
structure
and additional meta data as data.frame
.
BSFDataSet(ranges, meta, signal, forceEqualNames = TRUE) BSFDataSet(ranges, meta, signal, forceEqualNames = TRUE) BSFDataSetFromBigWig(ranges, meta, silent = FALSE)
ranges |
a |
meta |
a |
signal |
a |
forceEqualNames |
to maintain the integrity of chromosome names (TRUE/ FALSE). The option ensures that chromosome names present in the GRanges are also all present in the signal list and vice versa. Chromosomes names present in only the signal list or the ranges are removed. |
silent |
suppress loading message (TRUE/ FALSE) |
The ranges are enforced to have to have a "+" or "-" strand annotation,"*" is not allowed. They are expected to be of the same width and a warning is thrown otherwise.
The meta information is stored as data.frame
with at least two
required columns, 'id' and 'condition'. They are used to build the unique
identifier for each replicate split by '_' (eg. id = 1 and condition = WT
will result in 1_WT).
The meta data needs to have the additional columns 'clPlus' and 'clMinus'
to be present if BSFDataSetFromBigWig
is called.
It is used to provide the location to the iCLIP coverage
files to the import function. On object initialization these files are
loaded and internally represented in the signal slot of the object
(see BSFDataSet
).
The iCLIP signal is stored in a special list structure.
At the lowest level crosslink counts per nucleotide are stored as
Rle
per chromosome summarized as a SimpleRleList
. Such a list
exits for each replicate and must be named by the replicate identifier
(eg. 1_WT). Therefore this list contains always exactly the same number of
entries as the number of replicates in the dataset. Since we handle strands
initially seperated from each other this list must be given twice, once
for each strand. The strand specific entries must be named 'signalPlus' and
'signalMinus'.
A BSFDataSet object.
# load data files <- system.file("extdata", package="BindingSiteFinder") load(list.files(files, pattern = ".rda$", full.names = TRUE)) rng = getRanges(bds) sgn = getSignal(bds) mta = getMeta(bds) bdsNew = BSFDataSet(ranges = rng, signal = sgn, meta = mta)