User: sj1

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sj110
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2 years, 9 months ago
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3 years, 2 months ago
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s**@nibmg.ac.in

Posts by sj1

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Comment: C: Regarding Somatic Mutation Signature
... This is the required output of sessioninfo - > sessionInfo() R version 3.2.4 (2016-03-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale:  [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN         [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSA ...
written 2.8 years ago by sj110
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Regarding Somatic Mutation Signature
... Hi Sir, While running the somatic signature package,I am getting an error - > sigs_nmf = identifySignatures(sca_mm, n_sigs, nmfDecomposition) Error in rowQ(imat, ncol(imat)) : cannot handle missing values. Calls: identifySignatures ... standardGeneric -> eval -> eval -> eval -> rowM ...
mutational signature somatic signature written 2.8 years ago by sj110 • updated 2.8 years ago by Julian Gehring1.3k
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Comment: C: Regarding Somatic Mutation Signature
... A gentle reminder sir,if you could solve the above problem then it would be very helpful for us. Swati ...
written 2.8 years ago by sj110
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Comment: C: Regarding Somatic Mutation Signature
... Thanks for your response. I am getting an error - > sigs_nmf = identifySignatures(sca_mm, n_sigs, nmfDecomposition) Error in rowQ(imat, ncol(imat)) : cannot handle missing values. Calls: identifySignatures ... standardGeneric -> eval -> eval -> eval -> rowMax -> rowQ -> rowQ I ...
written 2.9 years ago by sj110
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Comment: C: Regarding Somatic Mutation Signature
... Thanks for your reply. There are several Data sets present in the package SomaticCancerAlterations and one of them is gbm_tcga which is a GRanges object.You have run this package for all the datasets.While exporting the gbm_tcga dataset I have converted it into a dataframe to see the structure of t ...
written 2.9 years ago by sj110
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Regarding Somatic Mutation Signature
... Hi Sir, For plotMutationSpectrum function,I want to know the exact process of calculating contribution. Regarding second question I have run the same code 10 times,please have a look at the link for the code https://www.dropbox.com/s/sug1i8v1zoqm1ce/Mutation_signature_package_data.R?dl=0 Please h ...
somaticsignatures written 2.9 years ago by sj110 • updated 2.9 years ago by Julian Gehring1.3k
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Comment: C: Regarding somatic signature package
... Hi Sir, For plotMutationSpectrum function,I want to know the exact process of calculating contribution. Regarding second question I have run the same code 10 times,please have a look at the link for the code https://www.dropbox.com/s/sug1i8v1zoqm1ce/Mutation_signature_package_data.R?dl=0 Please h ...
written 2.9 years ago by sj110
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Answer: A: Regarding somatic signature package
...   Hi Sir, Please have a look at this link https://www.dropbox.com/s/p30pdl0a7ifdv7a/ss1_ss2.png?dl=0 where I have attached an image of two plots which are slightly different to each other. I have used this function plotSignatures(sigs_nmf) + ggtitle("Somatic Signatures: NMF - Barchart") and run t ...
written 2.9 years ago by sj110
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Comment: C: Regarding somatic signature package
... I have to send plots but I am not getting any attachment option here.Plz help.Also I need the answer of first question, what does contribution means for this plot fuction plotMutationSpectrum(sca_motifs, "study") as it gives Contribution vs Motif plot. ...
written 2.9 years ago by sj110
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Regarding somatic signature package
... Hi Sir, The previous problem is solved,thanks for your effort.I have a question the plot that is generated for Mutation spectrum using this function - plotMutationSpectrum(sca_motifs, "study") gives Contribution vs Motif plot.What does Contribution means here? Another Question regarding Mutation ...
somaticsignatures written 2.9 years ago by sj110 • updated 2.9 years ago by Julian Gehring1.3k

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