Comments (5)
PoisonAlien
commented on July 17, 2024
Hi,
It's a known bug report #22
I will fix it by weekend. Can you just check if you're getting same error using only one of the gistic file (either amp or del) ?
m = read.maf(maf = "tcga_lohr_namefix_cut.maf", useAll = TRUE, gisticAmpGenesFile ="amp_genes.conf_75.txt", gisticAllLesionsFile = "all_lesions.conf_75.txt")from maftools.
PoisonAlien
commented on July 17, 2024
Hi,
I can't seem to reproduce this error on my machine. Do you think you can share your file ?
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rdmorin
commented on July 17, 2024
Sure. I can privately share them with you. Is email OK?
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PoisonAlien
commented on July 17, 2024
Yes, email is ok. [email protected]
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PoisonAlien
commented on July 17, 2024
Hi Ryan,
I have made necessary changes and fixed gistic bugs. Can you install again from github and let me know ?
devtools::install_github(repo = 'poisonAlien/maftools')
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Related Issues (20)
- 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
- unknown tumor_sample_barcode
- extractSignatures
- filterMaf error
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