User: gaiusjaugustus

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Posts by gaiusjaugustus

<prev • 15 results • page 2 of 2 • next >
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Howto: View Pileup or Base level stats in R using Rsamtools or rbamtools
... Hello, I have 50 bam files that I'd like to go through.  I have a list of mutations in 21 genes in those bamfiles, and I'd like to write some code to go through each gene, locate the base that is mutated, and get a readout of what's there in the tumor sample and the normal sample. In the past I've ...
rsamtools rbamtools written 3.1 years ago by gaiusjaugustus0 • updated 3.1 years ago by li lilingdu450
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Comment: C: Genomic Ranges findOverlaps by sample
... I actually just realized I could use reduce() on the combined regions to do what I want to do, except that it won't keep my extra columns.  I tried translating your solution into  mapply(reduce, split(CombinedRegions, ~File)) but this doesn't work.  When I try just split(CombinedRegions, ~File), ...
written 3.1 years ago by gaiusjaugustus0
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Genomic Ranges findOverlaps by sample
... I have 2 (very similar but not identical) genomic ranges objects, each with up to 33 samples, that I am trying to find overlaps and combine in a particular way.  I'm trying to do this separately for each sample.  I know I could do this with a for loop: subsets <- c(1:33) for (i in subs ...
genomicranges written 3.1 years ago by gaiusjaugustus0 • updated 3.1 years ago by Michael Lawrence11k
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QC for Affymetrix Arrays
... I am currently using Aroma's ASCRMAv2 & Paired PSCBS to do a copy number analysis on Affymetrix GenomeWide SNP Array 6.0 data.  I've run the data through but haven't yet seen a measure of quality that will allow me to remove bad samples.   Using Affy's Genotyping Console, I can get MAPD values ...
affymetrix affymetrix microarrays aroma written 3.3 years ago by gaiusjaugustus0
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Clustering like samples with a lot of data
... I have a very large dataframe/matrix with >100 samples and >50,000 datapoints for each sample.  I'd like to cluster the samples to get an idea of which have similar patterns.  The data looks like this:   Row.names Region1   Region2 .....  Region N   P1                 3             3         ...
clustering written 3.5 years ago by gaiusjaugustus0

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