User: Wayne

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Wayne0
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Posts by Wayne

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derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
... Hi, I am trying to use derfinder to analyze samples from Saccharomyces cerevisiae. I am able to supply the species and chromosome style information in the `fullCoverage()` command, but when I go to do `regionMatrix()` the style has changed. This is my code to get to the `fullCoverage()` call: ## ...
derfinder written 2.5 years ago by Wayne0
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Comment: C: regionMatrix for derfinder crashes with seqnames issue on non-human data
... THIS IS MEANT TO REFERENCE A COMMENT I MADE IN MY QUESTION ABOUT WHAT I WAS ORIGINALLY TRYING TO DO: By the way, for anybody who came here because you are also trying this with yeast, or other non-human model organism, by providing the correct species name, but still encountering the error: Error ...
written 2.5 years ago by Wayne0
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Comment: C: regionMatrix for derfinder crashes with seqnames issue on non-human data
... Thanks, Leonardo.  That eliminated the `Error in .normargSeqlengths(value, seqnames(x)) :   when the supplied 'seqlengths' vector is named, the names must match the seqnames` error that was stopping the `regionMartrix()` command at the tenth chromosome, producing no results. Now I do indeed produce ...
written 2.5 years ago by Wayne0
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Comment: C: regionMatrix for derfinder crashes with seqnames issue on non-human data
... Okay I tried this command below: ## Load libraries library('derfinder') library('GenomicRanges') file_designations <- c("WT1","WT2","WT3", "MT1", "MT2", "MT3") chrs_all = c('I', 'II','III','IV', 'IX', 'V', 'VI', 'VII', 'VIII', 'X', 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI', 'XVII') ## Load the da ...
written 2.5 years ago by Wayne0
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regionMatrix for derfinder crashes with seqnames issue on non-human data
... Hi, I am trying to use derfinder to analyze samples from Saccharomyces cerevisiae. Something about the chromosome names is causing me issues when I get to building a regionMatrix.  However, in trying to bypass that issue to see if I could even get some expressed regions data, I think I uncovered an ...
genomicranges genomeinfodb derfinder written 2.5 years ago by Wayne0

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