Comments (4)
Hi,
Thanks for reporting this !
This was a mistake from my side, should have been more careful. You were right about adding hugo_symbol to barcodes. I have fixed it. Thanks again.
P.S: that after subsetting in the above example you may not be be able to draw heat maps or rainfall plots since you're left with only one sample.
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Hi,
Thanks a lot for fixing this so promptly! subsetMaf() and oncoplot()
now work as expected. However, I am still having issues with 'rainfallPlot()':
#import
> var.annovar.maf <- annovarToMaf(annovar = var.annovar, Center = 'CSI-NUS', refBuild = 'hg19', tsbCol = 'Tumor_Sample_Barcode', table = 'ensGene', header = TRUE, MAFobj=TRUE)
#plot
> rainfallPlot(maf=var.annovar.maf, detectChangePoints = TRUE, fontSize = 12, pointSize = 0.6)
Error in seg.spl[[1]] : subscript out of bounds
In addition: Warning message:
In is.factor(x) : NAs introduced by coercion
#check if more than one sample
> getSampleSummary(var.annovar.maf)
Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins Missense_Mutation total
1: fake_4 1 0 1 2
2: fake_5 0 1 1 2
3: fake_7 0 1 1 2
4: fake_1 0 0 1 1
5: fake_2 0 0 1 1
6: fake_3 0 0 1 1
7: fake_6 0 0 1 1
I was assuming the issue might be due to the low number of mutations in the test dataset, but I'm running into the same issue with my own, larger dataset with plenty of mutations...
Thanks again,
sribi
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Hi,
This was an issue with empty chromosomes. i.e, chromosomes with no variants resulted in error. I have fixed it. I would really appreciate if you could try installing it again and let me know if it works.
Target level branch, since I haven't merged it with master yet.
devtools::install_github(repo = "PoisonAlien/maftools", ref = 'devel')
Thanks again. This was helpful.
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Hi,
The bug in rainfallPlot()
, as described above, seems to be fixed in your latest push to devel!
Thanks for fixing it so quickly.
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Related Issues (20)
- Error in sub(re, "", x, perl = TRUE) : input string 78 is invalid UTF-8 in subsetMaf HOT 9
- Lollipop plots HOT 5
- is it possible to create a gisticChromPlot using mouse data? HOT 2
- clinicalEnrichment Error: Object 'Analysis' not found amongst [] HOT 7
- Incomplete population of labels in coGisticChromPlot; overlapping of labels that do populate HOT 2
- survGroup minSample option HOT 2
- when adding cntable to maf tools object, if no mutations in gene the Start_Position End_Position are blank leading to errors HOT 5
- Extracting VAF information apart from plot. HOT 4
- Running trinucleotideMatrix generates Error in.Call2 HOT 11
- Getting error in lollipop plot HOT 3
- Signature plot HOT 11
- TMB plot (tcgaCompare): Burden changes depending on input order HOT 2
- Different aa.lengths in lollipopPlot() and lollipopPlot2() HOT 2
- lollipopPlot()Report an error:Error in .getdomains(geneID = gene, refSeqID = refSeqID, proteinID = proteinID) : Structure for protein PPDPFL not found. HOT 1
- The get_col_df function seems to have a bug in the 6th line HOT 2
- Error in if (dist <= mergeDist) { : missing value where TRUE/FALSE needed HOT 1
- sampleSwaps.R: add an error message in case of missing index files HOT 6
- Lollipopplot does not show complete protein length. HOT 4
- Questions about MATH score HOT 1
- Error in get_lp_data(maf = m1, geneID = gene, AACol = AACol1, refSeqID = refSeqID, : Structure for protein BAGE3 not found. HOT 1
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