User: dktarathym

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dktarathym0
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Posts by dktarathym

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VariantAnnotation Package Code problem
... I am having problem in running a code from Variant Annotation Package: cds<- locateVariants(vcf, sacCer3_db_ens, AllVariants()) Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :    subscript contains NAs or out-of-bounds indices ...
R bioconductor written 5.1 years ago by dktarathym0 • updated 5.1 years ago by Valerie Obenchain6.7k
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Comment: C: Function for barplot
... My idea is that, I want to make a script, that would work to plot the mutation for vcf file(s). For example: if I have 1 vcf file, and I want to see the no. of mutations in it (for each chromosome), this script should print the barplot. In case, I have multiple files, say 5, it should plot mutations ...
written 5.1 years ago by dktarathym0
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Answer: A: Function for barplot
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written 5.1 years ago by dktarathym0
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Function for barplot
... Hi, I wrote some codes. Explanations are below:  # Loading required packages library("VariantAnnotation") library("TxDb.Scerevisiae.UCSC.sacCer3.sgdGene")   # args will take different values (VCF files) while running the script from command line  args <- commandArgs(trailingOnly = TRUE) fi ...
R written 5.1 years ago by dktarathym0
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Answer: A: ORF lengths using Yeast Annotation package
... Hi James, It works. Thank you so much. Best regards, Deepak ...
written 5.1 years ago by dktarathym0
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Dot Plot for a matrix
... I have a matrix.   Dimensions=> rows= 6534, columns= 6   rows are the ORF (yeast)   columns are the name of the vcf files of yeast.   This matrix stores the information of no. of mutations occurring for a particular gene in each file (0 means, there is no mutation of that particular gene ...
R bioconductor written 5.1 years ago by dktarathym0
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Answer: A: ORF lengths using Yeast Annotation package
... HI Marc, Yes, it worked. Thank you so much. Best regards, Deepak ...
written 5.1 years ago by dktarathym0
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ORF lengths using Yeast Annotation package
... Hi, I am trying to find out length of Yeast ORF. Where is my mistake? > sacCer3Length <- function(symbols) { require(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene) require(org.Sc.sgd.db) exons.db = exonsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by='gene') egs = unlist( mget(symbols[ s ...
yeast genomicranges written 5.1 years ago by dktarathym0

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