Comments (3)
We should change computeStat()
in the following way. The default should be to always report f-statistics. We will add an argument to ask for t-statistics instead (which should cause an error if length(coef)>1
). Note that the output of computeStat()
do already store what kind of stats are being computed; it has a $stat.type
with values either "fstat"
or "tstat"
in addition to the actual statistics stored in $stat
from bsseq.
Also, if BSmooth.fstat()
is used to analyse a two-group model (i.e., ncol(design) == 2
), then cutoff
rather than cutoff ^ 2
applies since this is simply a t-statistic (https://github.com/kasperdanielhansen/bsseq/blob/master/R/BSmooth.fstat.R#L84)
from bsseq.
You could test for this by looking at $stat.type. which happens before we
set cutoff.
On Tue, Aug 30, 2016 at 6:02 PM, Peter Hickey [email protected]
wrote:
Also, if BSmooth.fstat() is used to analyse a two-group model (i.e., ncol(design)
== 2), then cutoff rather than cutoff ^ 2 applies since this is simply a
t-statistic (https://github.com/kasperdanielhansen/bsseq/blob/
master/R/BSmooth.fstat.R#L84)—
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Related Issues (20)
- read.bismark() too slow - input format issue? HOT 8
- BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment HOT 2
- Error: C stack usage 10847362 is too close to the limit HOT 3
- Is it possible to append metadata to the GRanges within BSseq objects? HOT 3
- Normalization of the WGBS smooth data HOT 5
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- Error BSmooth HOT 3
- read.bismark: option to change tmpdir in fread? HOT 4
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- combineList: BACKEND Argument not working as intended HOT 1
- BSmooth.tstat issue HOT 11
- Updating beachmat to tatami HOT 1
- combine(sample1.smooth, sample2.smooth) gives in unsmooth results? HOT 4
- bsmooth() fails - Error in `h()`: ! error in evaluating the argument 'seed' in selecting a method for function 'DelayedArray': HDF5. File accessibility. Unable to open file. HOT 3
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- error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark. HOT 26
- Represent a CpG with single row during import HOT 11
- exclude "Y" chromosome from bsseq object HOT 3
- Upcoming change to DelayedArray::realize() HOT 2
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