User: arsala521

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arsala52110
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Posts by arsala521

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Comment: C: Observing composition of somatic signatures as barcharts
... Actually for the previous plots I constructed, things worked simply in the way that when I entered the command for plotting, the accurate pdf file of the plot was created in the working directory. However things didn't go well so smoothly with this command and file created in working directory had z ...
written 3.2 years ago by arsala52110
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Observing composition of somatic signatures as barcharts
... Hello I am using SomaticSignature package in my study. After decomposition and inferring of signatures, I tried to visualize the signatures as heatmap and as barchart. The hetamap was generated successfully but not the barchart. I used the following command to construct barchart: plotSignatures(s ...
somaticsignatures written 3.2 years ago by arsala52110
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Comment: C: Assesment of the number of signatures when using SomaticSignatures package
... I did try with 2:4. I got the plot but I was bit confused in choosing the number of signatures from the given plot. As number of signatures has to be chosen such that with increasing the number of signatures the RSS and the explained variance do not change sufficiently. When I plotted using n_sigs= ...
written 3.2 years ago by arsala52110
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Assesment of the number of signatures when using SomaticSignatures package
... Hello I am analyzing data through SomaticSignatures package. I am trying to use assesNumberSignatures function to determine number of signatures. I entered the following commands: > n_sigs = 2:8 > gof_pca = assessNumberSignatures(cancer_mm, n_sigs, pcaDecomposition​) When I entered the sec ...
assesnumbersignatures somaticsignatures package written 3.2 years ago by arsala52110 • updated 3.2 years ago by Wolfgang Huber13k
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Comment: C: Number of tumor samples and analysis by SomaticSignature Package
... Thank you so much. ...
written 3.3 years ago by arsala52110
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Number of tumor samples and analysis by SomaticSignature Package
... Hello I am using SomaticSignatures package for data analysis. If I have four cancers under study should the number of samples for each cancer type be the same. I mean to ask that is this alright if for one cancer type I have data for 200 samples and for other cancer type I have data for 400 samples ...
somaticsignatures written 3.3 years ago by arsala52110 • updated 3.3 years ago by Julian Gehring1.3k
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Comment: C: Sequence Context of Somatic Variants
... Thank you so much   ...
written 3.3 years ago by arsala52110
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Sequence Context of Somatic Variants
... Hello I am using SomaticSignatures package. When we extract sequence context of single nucleotide variants using the command like this sca_motifs = mutationContext(sca_vr, BSgenome.Hsapiens.1000genomes.hs37d5) we get two additional columns in vranges, alteration and context. If ref is G and alt ...
somaticsignatures mutation context written 3.3 years ago by arsala52110 • updated 3.3 years ago by Julian Gehring1.3k
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Comment: C: vcf to vranges
... thank you so much.   ...
written 3.3 years ago by arsala52110
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vcf to vranges
... Hello I made vranges object from my VCF file usingreadVcfAsVRanges. There are 37974 variants in the VCF file and in vranges there are 14682016 ranges. Can someone please explain this difference? I guess that if a variant is in more than one sample then there will be more than one range for that va ...
readvcfasvranges vcf to vranges written 3.3 years ago by arsala52110 • updated 3.3 years ago by Valerie Obenchain6.7k

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