I am a complete newbie in data science and R but I have been trying to use the script to analyze CNA for a targeted capture sequencing in cfDNA as following:
Correcting Tumour
Removed 121 bins near centromeres.
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Filtering low uniqueness regions with mappability score < 0.9
Removed 1 bins near centromeres.
Determining gender...Gender female
Outputting to: .//tumor_sample.correctedDepth.txt
Warning messages:
1: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
span too small. fewer data values than degrees of freedom.
2: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.36574
3: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 0.0032647
4: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
5: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 0.0033244
6: In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
runEM: Initialization
runEM iter1: Expectation
Error in runEM(dataMat, chr, chrInd, param, maxiter, verbose, estimateNormal = estimateNormal, :
INTEGER() can only be applied to a 'integer', not a 'NULL'
Calls: HMMsegment -> runEM
Execution halted
and when running without using a bed file it works but gives the following warnings:
1: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin, :
Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
2: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin, :
Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
3: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin, :
Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
4: In KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin, :
Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Hi,
I am a complete newbie in data science and R but I have been trying to use the script to analyze CNA for a targeted capture sequencing in cfDNA as following:
and I am keep getting the following error:
and when running without using a bed file it works but gives the following warnings:
my .BED file looks like this
I'll appreciate your advice. Bests, Mouhamad