Displaying 7 results from an estimated 7 matches for "intron".
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intro
2010 Apr 29
1
Using plyr::dply more (memory) efficiently?
...8131 99 0 utr 0
WASH5P WASH5P chr1
10 14601 154 0 utr 0
WASH5P WASH5P chr1
11 19184 50 0 utr 0
WASH5P WASH5P chr1
12 4693 140 36 intron 2
WASH5P WASH5P chr1
13 4902 757 36 intron 1
WASH5P WASH5P chr1
14 5811 659 144 intron 47
WASH5P WASH5P chr1
15 6629 92 21 intron 1
WASH5P WASH5P chr1
16 691...
2011 Nov 15
1
Problem with substr
...tmp.subject,type="local") # align all exons pairwise to gene
sequence
tmp.start<-start(subject(tmp.align)) # vector of all alignment
starts
tmp.end<-end(subject(tmp.align)) # vector of all alignment ends
for(ex in 1:(length(tmp.end)-1)){ # extract introns
tmp.intron<-substr(tmp.subject,tmp.end[ex]+1,tmp.start[ex+1]-1)
introns<-rbind(introns,cbind(tmp.id,tmp.end[ex]+1,tmp.start[ex+1]-1,tmp.intron))
}
}
Thank you
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2008 Feb 21
3
variable syntax problem
...;red", "blue"), by.order=TRUE,
scale.to.gene=FALSE, use.symbol=TRUE, use.mt=FALSE, *main="PDE1A
(red=prostate, blue=tissues[i])"*, ylab="intensity / probeset",
exon.y=1, exon.height=1, exon.bg.col="#c3c3c3",
exon.bg.border.col="black", show.introns=TRUE)
y=y-3
z=z-3
dev.off() }
when i write main=tissues[i] the value is written right. but i would
like to have an additional text...
thanks
paul
[[alternative HTML version deleted]]
2007 Apr 24
0
new version of seqinR
...ot nucleotide skews
on artificially rearranged prokaryotic chromosomes.
o New function gbk2g2.euk() available. Similarly to gbk2g2(), this function
extracts the coding sequence annotations from a GenBank format file. This
function is specifically designed for eukaryotic sequences, i.e. with
introns.
The output file will contain the coordinates of the exons, along with the
name of the CDS to which they belong.
o After an e-mail by Marcelo Bertalan on 26 Mar 2007, a bug in oriloc()
when
the gbk argument was NULL was found and fixed by Anamaria Necsulea.
o Functions translate() and get...
2007 Apr 24
0
new version of seqinR
...ot nucleotide skews
on artificially rearranged prokaryotic chromosomes.
o New function gbk2g2.euk() available. Similarly to gbk2g2(), this function
extracts the coding sequence annotations from a GenBank format file. This
function is specifically designed for eukaryotic sequences, i.e. with
introns.
The output file will contain the coordinates of the exons, along with the
name of the CDS to which they belong.
o After an e-mail by Marcelo Bertalan on 26 Mar 2007, a bug in oriloc()
when
the gbk argument was NULL was found and fixed by Anamaria Necsulea.
o Functions translate() and get...
2002 Nov 27
0
R genetics package now available
...marker(name="A1691G",
+ type="SNP",
+ locus.name="MBP2",
+ chromosome=9,
+ arm="q",
+ index.start=35,
+ bp.start=1691,
+ relative.to="intron 1")
>
>
[...]
>
> data$g1 <- genotype(data$g1, locus=c104t)
> data$g2 <- genotype(data$g2, locus=a1691g)
> data$g3 <- genotype(data$g3, locus=c2249t)
>
> data
y g1 g2 g3
1 -0.084796634 T/T G/G T/C
2 1.454537575 C/C G/G T/T
3 -0.899625...
2002 Nov 27
0
R genetics package now available
...marker(name="A1691G",
+ type="SNP",
+ locus.name="MBP2",
+ chromosome=9,
+ arm="q",
+ index.start=35,
+ bp.start=1691,
+ relative.to="intron 1")
>
>
[...]
>
> data$g1 <- genotype(data$g1, locus=c104t)
> data$g2 <- genotype(data$g2, locus=a1691g)
> data$g3 <- genotype(data$g3, locus=c2249t)
>
> data
y g1 g2 g3
1 -0.084796634 T/T G/G T/C
2 1.454537575 C/C G/G T/T
3 -0.899625...