Displaying 20 results from an estimated 78 matches for "hsa".
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2009 Sep 29
4
How can I avoid a for-loop through sapply or lapply ?
Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following:
> nml
[1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a"
[2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b"
[3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c"
[4] "hsa-let-7d MIMAT0000065 Homo sapiens let-7d"
[5] "hsa-let...
2008 Nov 06
1
replacing values in a vector
Hello list.
I have a vector of values:
eg
> head(diff_mirs_list)
[1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a"
[6] "hsa-miR-29b"
and I would like to conditionally replace each value in this vector with a number defined in a dataframe:
> fc
???????????? Probe ave.fc
1?????? hsa-let-7a?...
2013 Jan 27
2
rpart
...ll:
rpart(formula = mydata$class ~ ., data = as.data.frame(t(mydata)))
? n= 62
???????? CP nsplit rel error??? xerror????? xstd
1 0.6363636????? 0 1.0000000 1.0000000 0.1712469
2 0.1363636????? 1 0.3636364 0.6818182 0.1532767
3 0.0100000????? 2 0.2272727 0.7727273 0.1596659
Variable importance
? Hsa.627?? Hsa.692 Hsa.692.2? Hsa.3306?? Hsa.601?? Hsa.831? Hsa.1832? Hsa.2456
?????? 19??????? 13??????? 11??????? 10??????? 10???????? 8???????? 6???????? 6
?Hsa.8147? Hsa.1131 Hsa.692.1
??????? 6???????? 5???????? 5
Node number 1: 62 observations,??? complexity param=0.6363636
? predicted class=...
2011 Sep 30
1
Hi
Hi,
There is a question that I am confused.
I have a set of data like this:
hsa-miR-205--GATA3 0.797882767 1.08E-13
hsa-miR-205--ITGB4 0.750217593 1.85E-11
hsa-miR-187--PGF 0.797604155 3.24E-11
hsa-miR-205--SERPINB5 0.744124886 3.28E-11
hsa-miR-205--PBX1 0.734487224 7.89E-11
hsa-miR-205--MCC 0.72499934 1.80E-10
hsa-miR-205--WNT5B 0.717705259 3.33E-10
hsa-miR-200c...
2010 May 27
3
how to extract the 1st field from a vector of strings
I have the following vector of strings (shown only the first 3 elements)
> desc[1:3]
[1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a"
[2] "hsa-let-7a* MIMAT0004481 Homo sapiens let-7a*"
[3] "hsa-let-7a-2* MIMAT0010195 Homo sapiens let-7a-2*"
> is.vector(desc)
[1] TRUE
> A <- unlist(strsplit(desc[1:3], " "))
> A
[1] "hsa-let-7a...
2012 Nov 01
1
GraphNEL object retrieve edgenumber from acc() or is it list of lists?
...everyone,
Im working with graphNEL object and want to extract all the nodes which
have adjacent nodes with at least 20 nodes in between them.
acc(graph, graphnodes) obviously provides a list for the accessable
nodes of every node from a node and a number of the edges between them.
Like this:
$`hsa:8379`
hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945
1 1 1 1 1
hsa:51433 hsa:51434 hsa:51529 hsa:64682 hsa:8697
1 1 1 1 1
$`hsa:51...
2011 Aug 15
3
Plot from function
...quot;,"a","b","b","c","c","d","d","e","e","f","f"))
}/
*The function is supposed plot a row from the following input-table:*
/ X1h X4h X9h X15h X18h X21h
hsa-miR-99b* 173 64 66 56 65 65
hsa-miR-99b 549 697 1070 1051 1777 2201
hsa-miR-99a* 3 1 3 0 3 2
hsa-miR-99a 5 4 14 16 33 37
hsa-miR-98 3475 4177 4075 4513 4631 5940
hsa...
2013 Jul 10
2
Replacing part of delimited string with R's regex
I have the following list of strings:
name <- c("hsa-miR-555p","hsa-miR-519b-3p","hsa-let-7a")
What I want to do is for each of the above strings
replace the text after second delimiter with "zzz".
Yielding:
hsa-miR-zzz
hsa-miR-zzz
hsa-let-zzz
What's the way to do it?
[[alternative HTML version deleted]]
2011 Sep 06
2
subsetting tables
Hi guys,
one of the questions where you need a real human instead of a search engine,
so it would be great if you could help.
I have a matrix of z-scores which I would like to filter, sometimes
columnwise, sometimes rowwise. Data looks like this:
Allstar hsa.let.7a hsa.let.7a.1 hsa.let.7a.2
2 0.87 0.79 -0.57 1.07
3 0.67 -1.14 -0.78 -0.95
4 -0.46 -0.30 -0.36 1.14
Now I want to find all elements which are below/above some threshold. Subset
works fine with the columns:
> subset(red[,...
2010 Dec 17
1
help with function
...ulMetric')
? ? #return whole list
? ? return(listMetric)
}
deMirPresGenes looks like this:
Gene.ID? ? Gene.Symbol? ? Species.ID? ? miRNA? ? Site.type? ? UTR_start? ? UTR_end? ? X3pairing_contr? ? local_AU_contr? ? position_contr? ? context_score? ? context_percentile
22848? ? AAK1? ? 9606? ? hsa-miR-183? ? 2? ? 1546? ? 1552? ? -0.026? ? -0.047? ? 0.099? ? -0.135? ? 47
19? ? ABCA1? ? 9606? ? hsa-miR-183? ? 2? ? 1366? ? 1372? ? -0.011? ? -0.048? ? 0.087? ? -0.133? ? 46
20? ? ABCA2? ? 9606? ? hsa-miR-495? ? 2? ? 666? ? 672? ? -0.042? ? -0.092? ? -0.035? ? -0.33? ? 93
23456? ? ABCB10? ? 9606?...
2016 Mar 05
2
[AMDGPU] non-hsa intrinsic with hsa target
...#39;s because get_group_id() uses get_local_size
> _CLC_DEF size_t get_global_id(uint dim) {
> return get_group_id(dim)*get_local_size(dim) + get_local_id(dim);
> }
>
> in libclc/amdgcn, 'get_local_size' invokes r600-xxx intrinsics. I doubt
> that libclc ever supports hsa-runtime before.
>
>
> thanks,
> --lx
>
>
> On Sun, Mar 6, 2016 at 12:11 AM, 李弘宇 via llvm-dev <llvm-dev at lists.llvm.org
> > wrote:
>
>> Dear Developers,
>>
>> I compiled a OpenCL kernel before (on Nov. last year) like
>>
>> __kernel vo...
2016 Mar 05
2
[AMDGPU] non-hsa intrinsic with hsa target
...velopers,
I compiled a OpenCL kernel before (on Nov. last year) like
__kernel void g(__global float* array)
{
array[get_global_id(0)] = 1;
}
with libclc, which would originally use the instrinsics like
llvm.r600.read.local.size.x().
I executed the generated object file with one version of the hsa-runtime
[1] provided by Mr. Stellard, when there was more than one workgroup, the
output of the program wasn't correct at that time. I guessed this might be
because get_group_id() always returned 1 (not quite sure what was going on
at that time).
When I compile such cases using current llvm tr...
2006 Sep 01
1
Reading many files at once
dear group,
i have 100 files starting with 'hsa-*'.
ex. file:
fruit p-value
------------
apple 0.0003
orange 0.004
kiwi 0.0003
peach 0.0004
I want to read all these files and create a single
matrix. here each file may have different fruit names.
in the matrix i want to have a union of all fruits and
those should be the rows in...
2011 Jun 27
1
create a new data frame after comparing two columns of the previous data frame
Hi everyone,
I am trying to find a way to filter a table; If I am given for example the
following table:
> head(intra)
chr miRNA start end strand ACC hsa_ID
region region_start region_end gene_id transcrip_id
1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b";
exon 1102484 1102578 NR_029639 NR_029639
2 chr1 miRNA 1103243 1103332 + ACC="MI0000737"; ID="hsa-mir-200a";
exon...
2016 Apr 05
1
Heatmap Colnames
...ly my column names do not completely appear. Can you please send me the appropriate code to visualise them?
Many Thanks!
Nils
library(GMD)
dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)), EntryB=as.numeric(c(4.16,4.82,-1.82,-3.02,0.99,1.1,-3.31)))
rownames(dat)=c("hsa-miR-200c","hsa-miR-520b","hsa-miR-199a-3p","mmu-miR-124a","hsa-miR-302a","hsa-miR-454","mmu-miR-137")
colnames(dat)=c("24", "72")
heatmap.3(dat, srtCol=70)
ndat<-as.matrix(dat)
heatmap.3(ndat, Rowv=FALSE, C...
2011 Oct 04
1
a question about sort and BH
Hi,
I have two questions want to ask.
1. If I have a matrix like this, and I want to figure out the rows whose
value in the 3rd column are less than 0.05. How can I do it with R.
hsa-let-7a--MBTD1 0.528239197 2.41E-05
hsa-let-7a--APOBEC1 0.507869409 5.51E-05
hsa-let-7a--PAPOLA 0.470451884 0.000221774
hsa-let-7a--NF2 0.469280186 0.000231065
hsa-let-7a--SLC17A5 0.454597978 0.000381713
hsa-let-7a--THOC2 0.447714054 0.000479322
hsa-let-7a--SMG7...
2010 Dec 18
0
[BioC] problem with function
...t; fails.
> >>
> >> Christian
> >>
> >> On 12/17/10 10:59 PM, Iain Gallagher wrote:
> >>> Hi
> >>>
> >>> FC is the second column of the deMirs
> variable. deMirs
> >> is a dataframe with 2 columns - Probe (e.g.
> hsa-miR-145) and
> >> FC (e.g 1.45). Using 'with' allows me to use
> deMirs as an
> >> 'environment'. I thus don't have to pass FC
> explicitly.
> >>>
> >>> Cheers
> >>>
> >>> i
> >>>
> >>&g...
2005 Jul 07
1
Plotting Character Variable
Any ideas about the following problem:
I have a matrix (A) that looks like this:
gene_names values
hsa-mir-124 0.3
hsa-mir-234 0.1
hsa-mir-344 0.4
hsa-mir-333 0.7
..... .......
(This is a 2 by 22283 matrix: quite large)
I would like to plot the values, but output the gene_names as the plotting
symbol. I have tried regular x,y plo...
2018 Sep 05
4
Can I control HSA config generated by AMDGPU backend?
...;
>
>
> Thanks,
>
> Changdao
>
>
>
> On Mon, Sep 3, 2018 at 5:25 AM Tamazov, Artem <Artem.Tamazov at amd.com>
> wrote:
>
> Hello,
>
>
>
> Please look into https://llvm.org/docs/AMDGPUUsage.html.
>
>
>
> > My target is amdgpu--amdhsa.
>
>
>
> This means that the kernel(s) are to be executed on HSA compatible
> runtimes such as AMD’s ROCm.
>
>
>
> > ..."enable_sgpr_dispatch_ptr = 1". Can I do something to turn that off
> in the generated assembly file?
>
> > ...user argument is...
2006 May 16
0
[PATCH][SVM][5/5] add hsa for ucode
SVM patch to add a host save area per core for the hypervisor and also
for the microcode. The microcode area is not guaranteed to be
compatible with the vmcb layout, therefore will require it''s own
"scratch pad". Consolidate the per core areas into a single structure.
Applies cleanly to 10002.
Please apply to xen-unstable.hg.
Please apply to xen-3.0-testing.hg.