User: shivangi.agarwal800

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Posts by shivangi.agarwal800

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Query regarding TCGA samples
... Hi I want to look into the mutation profile of tumor samples obtained from TCGA. Looking deep into the sample barcodes, I found that the analyte codes of different samples are different, for e.g. Here is three sample ids from same study, but there analyte is different. > TCGA-A7-A0DB-01A-11**D ...
samples tcga written 11 days ago by shivangi.agarwal80040 • updated 11 days ago by Kevin Blighe31k
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Comment: C: Mutational landscape plot
... Hi I noticed one problem while plotting this plot. When I simply plotted data given [in the link][1], I noticed that the gene which is having two same types of mutation with different variant in the same sample is being shown in the plot only once. example, the gene MAP3K1 is having two frame shift ...
written 5 weeks ago by shivangi.agarwal80040 • updated 11 days ago by RamRS19k
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Comment: C: WGCNA analysis in normal and tumor case
... Ya, this module-trait relationship plot, I have got. But to perform regression analysis of module to tumorstatus, I am giving command like, but getting error glm(TumourNormalStatus ~ darkgreen, family=binomial(link='logit')) Error in eval(predvars, data, env) : object 'TumourNormalStatus' n ...
written 6 weeks ago by shivangi.agarwal80040
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Comment: C: Mutational landscape plot
... That is fine, but I need to plot these in waterfall plot itself. Can it be done? ...
written 6 weeks ago by shivangi.agarwal80040
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Comment: C: Mutational landscape plot
... It means that the mutations having deleterious functional impact. It is not a standard classification, but it can be predicted using different tools. I got the information from cbioportal. My concern is if we can show these mutations in the graph itself while giving its information in input file. ...
written 6 weeks ago by shivangi.agarwal80040
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Comment: C: Mutational landscape plot
... Ok, I got it. That is fine. But, among non-synonyms, if we want to indicate the lethal mutation in the plot itself, how it can be done? ...
written 6 weeks ago by shivangi.agarwal80040
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Comment: C: Mutational landscape plot
... But, in this case, its not like that, all missense mutations are not non-synonyms. ...
written 6 weeks ago by shivangi.agarwal80040
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Mutational landscape plot
... Hi I am trying to make waterfall plot using GenVisR as shown [here][1]. I just put an example data like sample gene_name amino.acid.change trv_type TCGA-BH-A0WA-01 BRCA1 X1559_splice splice_site_del TCGA-AN-A0XU-01 BRCA1 G1788V missense TCG ...
mutation plot written 6 weeks ago by shivangi.agarwal80040 • updated 11 days ago by RamRS19k
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Comment: C: WGCNA analysis in normal and tumor case
... Ok thanks, I am looking into some papers. But can you elaborate more point no.1. "for each module's eigenvalues, correlate (cor and cor.test) or regress (lm or glm) these to TumourNormal status (encoded as 1 and 0)" ...
written 6 weeks ago by shivangi.agarwal80040
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Comment: C: WGCNA analysis in normal and tumor case
... Ya, I meant to say that only. My data is arranged in .tsv format containing gene name in column and sample id in rows. My concern was that if we want to study the difference between two groups (control and tumor) then should we input data containing both groups or we input them separately. But as p ...
written 6 weeks ago by shivangi.agarwal80040

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