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# custom script by Igor Dolgolev at NYUMC | |
plotPCAWithSampleNames = function(x, intgroup="condition", ntop=500) | |
{ | |
library("genefilter") | |
library("lattice") | |
rv = rowVars(assay(x)) | |
select = order(rv, decreasing=TRUE)[seq_len(min(ntop, length(rv)))] |
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########################################## | |
## Intersect and Venn Diagram Functions ## | |
########################################## | |
## Author: Thomas Girke | |
## Last update: August 15, 2009 | |
## Utilities: | |
## (1) Venn Intersects | |
## Computation of Venn intersects among 2-20 or more sample sets using the typical | |
## 'only in' intersect logic of Venn comparisons, such as: objects present only in | |
## set A, objects present only in the intersect of A & B, etc. Due to this restrictive |
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>hairpin_1_fwd | |
GATCGGAAGAGCACACGTCTGAACTCCAGTC | |
>hairpin_1_revcomp | |
GACTGGAGTTCAGACGTGTGCTCTTCCGATC | |
>hairpin_2_fwd | |
ACACTCTTTCCCTACACGACGCTCTTCCGATC | |
>hairpin_2_revcomp | |
GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT | |
>Illumina_top | |
ACACTCTTTCCCTACACGACGCTCTTCCGATC |
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seqid | Name | ||
---|---|---|---|
5 | Transcript_10 | EDO31303 | |
9 | Transcript_100 | EDO42116 | |
19 | Transcript_101 | EDO42087 | |
24 | Transcript_102 | EDO43514 | |
39 | Transcript_103 | tr|A7SUP6|A7SUP6_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g217764 PE=4 SV=1 | |
58 | Transcript_105 | EDO33432 | |
60 | Transcript_107 | tr|A7S0C0|A7S0C0_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g184098 PE=4 SV=1 | |
61 | Transcript_109 | EDO49229 | |
71 | Transcript_11 | tr|A7RQ19|A7RQ19_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g239897 PE=4 SV=1 |
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