With bonus R code

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While vector-friendly, R's paste function has a few behaviors I don't particularly like.

One is using a space as the default separator:

> adjectives> paste(adjectives,"er")
> paste(adjectives,"er")
 "lean er"   "fast er"   "strong er"  #d'oh
> paste(adjectives,"er",sep="")
 "leaner"   "faster"   "stronger"

Empty vectors get an undeserved first class treatment:

> paste(indelPositions,"i",sep="")
 "i"
> indelPositions> paste(indelPositions,"i",sep="")
 "5i"...
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Granted, not a brilliant sysadmin mind at work here, but this might help someone someday.
Scientific Linux (SL) is built from Red Hat Enterprise Linux

See installation instructions here:
http://rstudio.org/download/server

$ sudo rpm -Uvh
http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
 password for leipzig: 
Retrieving
http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
warning: /var/tmp/rpm-tmp.S2RQAH: Header V3 RSA/SHA256 Signature, key ID
0608b895: NOKEY
Preparing...          ...
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Let me get this out of the way: I just love RStudio.Created by a team lead by JJ Allaire, a name that should ring a bell if you were involved in web development during the Clinton administration, RStudio is an R IDE that is actually designed for R from...

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Let me get this out of the way: I just love RStudio.Created by a team lead by JJ Allaire, a name that should ring a bell if you were involved in web development during the Clinton administration, RStudio is an R IDE that is actually designed for R from...

Read more »

My goal is to develop a means of detecting chromosome bias from a human BAM file.

Because I've been working with proprietary and novel plant genomes for the last three years, I haven't had the chance to use any of the awesome UCSC-based annotational features that have been introduced and refined in Bioconductor until now. I've returned to biomedical research...

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My goal is to develop a means of detecting chromosome bias from a human BAM file.

Because I've been working with proprietary and novel plant genomes for the last three years, I haven't had the chance to use any of the awesome UCSC-based annotational features that have been introduced and refined in Bioconductor until now. I've returned to biomedical research...

Read more »

The UCR guide is a little sparse with regard to getting basic information from readAligned.

I'd like to add to the general cookbook. If some bioc people out there can contribute some alignment recipes can fill me in on some more basics please comment:

alignedReads 
#how many reads did I attempt to align
#i don't think you can't get this from...
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The UCR guide is a little sparse with regard to getting basic information from readAligned.

I'd like to add to the general cookbook. If some bioc people out there can contribute some alignment recipes can fill me in on some more basics please comment:

alignedReads 
#how many reads did I attempt to align
#i don't think you can't get this from...
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I wrote an R function to do soft-trimming, right clipping FastQ reads based on quality.

This function has the option of leaving out sequences trimmed to extinction and will do left-side fixed trimming as well.

#softTrim
#trim first position lower than minQuality and all subsequent positions
#omit sequences that after trimming are shorter than minLength
#left trim to firstBase, (1 implies no left trim)
#input:...
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