User: anand_mt

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anand_mt80
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Posts by anand_mt

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to plot Oncoplot with out sorting
... Hi Seeker, maftools on bioconductor release branch doesn't support this, however the one on GitHub has this option. Install it from GitHub and plot as you would normally; oncoplot(maf = laml, genes = ('TP53', 'DNMT3A', 'NPM1', 'RUNX1', 'CEBPA'), keepGeneOrder = TRUE) Let me know if this is what ...
written 19 months ago by anand_mt80
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Answer: A: about MAFTOOLS and ComplexHeatmap
... Hi Bogdan, maftools uses complexheatmaps oncoprint source code but with little modifications to automate the plotting. However you can run oncoplot function with `writeMatrix = TRUE` which will write the underlying matrix to an output file. This file can be directly used as an input to complexheatm ...
written 20 months ago by anand_mt80
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Answer: A: Maftools required fields do not match with vignette
... Hi Silvia, Reference_Allele and Tumor_Seq_Allele2 are essential fields for some of the analysis such as signature and APOBEC enrichment estimation. Apologies on my part, I will update the vignette. But for now, you can just add two columns to your MAF file (you can populate them with NA or leave th ...
written 21 months ago by anand_mt80
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Answer: A: how to create cnTable in maftools ?
... Hi, Apologies for late reply. Did you figure it out ? cnTable should be a tsv file with above mentioned columns. Something like this:   genes tsb cn TTN TCGA.AB.2814 Amp NRAS TCGA.AB.2872 Del TP53 TCGA.AB.2957 Amp NPM1 TCGA.AB.2904 Del SMC3 TCGA.AB.2824 Amp S ...
written 2.0 years ago by anand_mt80
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Answer: A: about maftools and gene names
... 1. It doesn't parse Hugo_Symbols and uses them as is. I think in your case its due to annovar annotations, it assigned them to two different genes (or synonyms of same gene, not sure). I would highly suggest to use VEP as its much smarter and picks a prioritized canonical transcript. Or even better ...
written 2.2 years ago by anand_mt80
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Comment: C: about MAFTOOLS and MAF files
... yes that is correct. Silent variants will be kept separately from main maf file unless you specify to use them. You can access them any time at `MAF@silent` ...
written 2.2 years ago by anand_mt80
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Answer: A: about MAFTOOLS and MAF files
... Hi, You need to return it as an MAF object.  var.annovar.maf = annovarToMaf(annovar = "ann_test.txt", Center = 'STANFORD', refBuild = 'hg38', tsbCol = "Tumor_Sample_Barcode",table = 'refGene', MAFobj = TRUE) ...
written 2.2 years ago by anand_mt80
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Comment: C: too many genes with low read-counts as differential expressed in DESeq2
... Thank you. This has been informative. ...
written 2.6 years ago by anand_mt80
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Comment: C: too many genes with low read-counts as differential expressed in DESeq2
... Excellent! A lot to think about. Sorry one last question, in one of the comment above, you mentioned -  You can't just look at the normalized counts alone if you have batch variables in the design.  I understand that the batch variables are not reflected in normalized counts. Whats the rational be ...
written 2.6 years ago by anand_mt80
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Comment: C: too many genes with low read-counts as differential expressed in DESeq2
... Hi Michael, Thanks for detailed clarification! Yes, the drug being used here is global repressor, so huge change is expected, and we were looking for robust DEGs. For now I am using fold change threshold on top of fdr to filter out the list. I have one more question, Since most of the postdocs in ...
written 2.6 years ago by anand_mt80

Latest awards to anand_mt

Popular Question 22 months ago, created a question with more than 1,000 views. For too many genes with low read-counts as differential expressed in DESeq2
Scholar 2.2 years ago, created an answer that has been accepted. For A: about MAFTOOLS and MAF files
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: about MAFTOOLS and MAF files

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