User: sj1

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sj110
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2 years, 11 months ago
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3 years, 4 months ago
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s**@nibmg.ac.in

Posts by sj1

<prev • 18 results • page 2 of 2 • next >
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Comment: C: 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 after giving this function - plotMutationSpectrum(sca_motifs, "study") is Contribution vs Motif plot.What is contribution means here?? Another question regarding Mutat ...
written 3.1 years ago by sj110
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Comment: C: Regarding somatic signature package
... Input file i.e, the first argument is in tab separated matrix format. ...
written 3.4 years ago by sj110
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Comment: C: Regarding somatic signature package
... Executed in 2 ways- 1st one- > makeGRangesFromDataFrame("file location", +     keep.extra.columns=FALSE, +     ignore.strand=FALSE, +     seqinfo=NULL, +     seqnames.field=c("chromosome"), +     start.field=c("start"), +     end.field=c("end"), +     starts.in.df.are.0based=FALSE) Error in .fi ...
written 3.4 years ago by sj110
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Comment: C: Regarding somatic signature package
... Hi, I have executed this and getting an error Error in .normarg_field(seqnames.field, "seqnames") :   object 'chromosome' not found Executed this command - > makeGRangesFromDataFrame("file location", +     keep.extra.columns=FALSE, +     ignore.strand=FALSE, +     seqinfo=NULL, +     seqnames ...
written 3.4 years ago by sj110
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Comment: C: Regarding somatic signature package
... I have successfully exported gbm_tcga dataset in a dataframe format.Now I want to create a GRange object but I am getting an error Error in .find_start_end_cols(df_colnames0, start.field0, end.field0) :   cannnot determine start/end columns executed command is - makeGRangesFromDataFrame("location ...
written 3.4 years ago by sj110
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Comment: C: Regarding somatic signature package
... Thanks for your response,it is really helpful.One more query is my input file is a .txt format then how to create a GRange object of a .txt file.  ...
written 3.4 years ago by sj110
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Comment: C: Regarding somatic signature package
... To export one of the dataset of the SomaticSignatures package dataset in R I have used this command data(sca_mm) write.table(sca_mm, "/location to store data/sca_mm.txt", sep="\t"), this is working fine but while exporting one of the dataset of SomaticCancerAlterations package using data(gbm_tcga ...
written 3.4 years ago by sj110
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Regarding somatic signature package
... Hi, I have gone through your paper, Inferring Somatic Signatures from Single Nucleotide Variant Calls and I want to run somatic signature package on the exome samples.Sir, I want to know the structure of the input file,the problem that I am facing is not able to export the datasets of the SomaticCa ...
somatic signature written 3.4 years ago by sj110 • updated 3.4 years ago by Julian Gehring1.3k

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