Being 33SuperWoman
Focus, if not now when? Start broad then narrow down - e.g. programming - R - functions!, form manageable tasks rather than wild unrealistic dreams.
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Working with VCFs in Bioconductor
library(VariantAnnotation)
vcf <- readVcf("GHS025_D1EH2ACXX_ATCACG_L001_R1.fastq.gz.dedupe.reorder.rg.recal.realign.snpeff.vcf", "hg19")
# reduce the set to those not present in the unaffected, for each family
# so not in GHS026, and in GHS025 and GHS027
# so not in GHS031, and in GHS015 and GHS008
# so not in GHS034, and in GHS036 and GHS033
3:07 PM | Filed Under | 0 Comments
10/1/2013
bin/circos -conf nameofconffile
result <- do.call(rbind, (genesymbols))
6:30 PM | Filed Under | 0 Comments
7/1/2013
Technical replicates and limma:
https://stat.ethz.ch/pipermail/bioconductor/2010-March/032535.html
https://stat.ethz.ch/pipermail/bioconductor/attachments/20110624/2da3f1ee/attachment.pl
7:25 PM | Filed Under | 0 Comments
2/01/2013
A
hypergeometric test is equivalent to a one-tailed
Fisher's Exact test.
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1:47 PM | Filed Under | 0 Comments
Learning R
Beginning at the beginning:
R inferno - nice pdf, probably helps if you are already a programmer.
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Youtube!
apply, effectively removes the need for a double for loop.
tapply expects vectors.
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This is wrong!:
mean(2, -100, -4, 3, -230, 5)
This is correct!:
mean(c(2, -100, -4, 3, -230, 5))
7:48 PM | Filed Under | 0 Comments