User: Inigo Martincorena

Reputation:
190
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Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
https://www.sanger.ac....
Twitter:
imartincorena
Last seen:
4 weeks ago
Joined:
5 months ago
Email:
i**@sanger.ac.uk

Posts by Inigo Martincorena

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Which Driver-Gene Detecting Software Supports hg38?
... Hello. [dNdScv][1], which I developed, supports GRCh38. Although it uses hg19 by default, the package contains the files and instructions to run GRCh38, as well as functions to run it on any assembly or species. In benchmarking analyses by PCAWG (the ICGC/TCGA pancancer analysis of whole genomes con ...
written 29 days ago by Inigo Martincorena190
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Do you mean running an analysis to detect significantly mutated non-coding regions? Unfortunately, the dNdScv package only works on coding mutations at the moment, although I may published a new function (called NBR) to do this in the near future. There are some methods out there to do what you say, ...
written 4 months ago by Inigo Martincorena190
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Comment: C: Removing duplicated mutations from a txt
... Friederike is correct that unique(df) will only remove duplicated rows, which may be your problem (as you say), in which case using unique(df) you will have corrected it. The warning by dndscv is slightly confusing since it will also be triggered by duplicated rows (I should make it clearer). Fried ...
written 4 months ago by Inigo Martincorena190
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Comment: C: Removing duplicated mutations from a txt
... Hello. Just a small clarification regarding the sentence: > Do not remove duplicates, dndscv keeps only one mutation per gene, > regardless of number of sample numbers dNdScv does not only keep one mutation per gene. By default, the dndscv function keeps up to 3 mutations per gene per sampl ...
written 4 months ago by Inigo Martincorena190
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... To avoid incurring into multiple testing problems, I would recommend using "qallsubs_cv", which combines the evidence from missense and truncating substitutions. You can see that TP53 has a very low qallsubs_cv (<0.001), while CHST2 is borderline or non-significant (0.0905). The q-value that you ...
written 4 months ago by Inigo Martincorena190
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Can you show the output table (sel_cv) for this gene (feel free to remove the gene name if you want to keep it anonymous)? It is hard to tell without seeing the data, since there can be artefacts affecting the reliability of some results. But, yes, dNdScv can sometimes successfully identify recurre ...
written 4 months ago by Inigo Martincorena190
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Not really, when calculating p-values for 20,000 genes, you expect many (~1,000) to have p-values<0.05 by chance. q-values are corrected for multiple testing to avoid this and so q-values should always be used. You can use a less conservative q-value cutoff (e.g. 0.10) but I would be careful as y ...
written 4 months ago by Inigo Martincorena190 • updated 4 months ago by RamRS22k
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Hello, The outputs that you are asking for are not standard outputs from dndscv. They can be obtained with some additional calculations based on the outputs of dNdScv and following the methods of [my paper in Cell][1]. However, the risk of these measures being misused or misinterpreted by users with ...
written 4 months ago by Inigo Martincorena190 • updated 4 months ago by RamRS22k
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... You can certainly try dNdScv, running it separately on each set of patients and on both sets together. This will give you lists of significant genes and some measure of selection. However, dNdScv is not designed to look for differences between two cohorts, so you may want to consider alternative app ...
written 5 months ago by Inigo Martincorena190
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... I would need to know more about your project to give you a good answer. It all depends on how clean your table of somatic mutations is. Many false positives and artefacts tend to have low allele frequencies, and filtering them out may improve the results. However, if your dataset is clean, you don't ...
written 5 months ago by Inigo Martincorena190

Latest awards to Inigo Martincorena

Teacher 29 days ago, created an answer with at least 3 up-votes. For A: dNdScv error: Zero coding substitutions found in this dataset
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Removing duplicated mutations from a txt
Scholar 5 months ago, created an answer that has been accepted. For A: dNdScv error: Zero coding substitutions found in this dataset
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: dNdScv error: Zero coding substitutions found in this dataset

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