User: jpluta26

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jpluta260
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Posts by jpluta26

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Comment: C: Combining GRange/VRange objects
... this was it exactly. thank you!! ...
written 3.6 years ago by jpluta260
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Combining GRange/VRange objects
... I'm working on extracting somatic signatures from a group of tumor data. I was able to do this with one dataset pretty easily, I just read in the vcf files and concatenated with c(). Example: dat1 <- readVcfAsVRanges(file1.vcf, seqinfo(file1)) vr_1 <- mutationContext(dat1, ref) dat2 <- r ...
somaticsignatures granges vranges readvcfasvranges written 3.6 years ago by jpluta260 • updated 3.6 years ago by Michael Lawrence11k
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Comment: C: SomaticSignatures - Getting Started & Trouble Shooting
... thanks for the reply, it was helpful. i was able to get some basic code working using the BSgenome reference package. the SomaticSignatures vignette states that a Fasta file can be used naturally, and i have this for each subject, so i was hoping to incorporate that. maybe i can figure out how to in ...
written 3.6 years ago by jpluta260
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SomaticSignatures - Getting Started & Trouble Shooting
... Hello, I am new to using bioconductor and new to genetics in general- sorry if this is an obvious question. I am trying to get started using the SomaticSignatures package. I have several TCGA subjects with .vcf files, and each subject has a .bam sequence file. I understand I need to load both the se ...

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