Displaying 6 results from an estimated 6 matches for "alphaproteobacteria".
2007 Oct 11
1
creating summary functions for data frame
...Bacteria
3 NC_009484 cir 0.6799 1790000 773000 3389227 Bacteria
4 NC_009484 cir 0.6799 1790000 773000 3389227 Bacteria
5 NC_009484 cir 0.6799 1790000 773000 3389227 Bacteria
grp feature gene begin dir gc_content replicor LEADLAG
1 Alphaproteobacteria CDS CDS 261 + 0.654244 RIGHT LEAD
2 Alphaproteobacteria CDS CDS 1737 - 0.651408 RIGHT LAG
3 Alphaproteobacteria CDS CDS 2902 + 0.607843 RIGHT LEAD
4 Alphaproteobacteria CDS CDS 3693 + 0.617647 RIGHT LEAD
5 Alphaproteobacteria CDS...
2007 Sep 19
2
function on factors - how best to proceed
...1790000 773000 3389227 Bacteria
3 NC_009484 cir 1790000 773000 3389227 Bacteria
4 NC_009484 cir 1790000 773000 3389227 Bacteria
5 NC_009484 cir 1790000 773000 3389227 Bacteria
grp feature gene begin dir gc_content replicor LEADLAG
1 Alphaproteobacteria CDS CDS 261 + 0.654244 RIGHT LEAD
2 Alphaproteobacteria CDS CDS 1737 - 0.651408 RIGHT LAG
3 Alphaproteobacteria CDS CDS 2902 + 0.607843 RIGHT LEAD
4 Alphaproteobacteria CDS CDS 3693 + 0.617647 RIGHT LEAD
5 Alphaproteobacteria CDS...
2012 Mar 02
2
Why do my regular expressions require a double escape \\ to get a literal??
...ontains taxonomical data of bacteria
in hierarchical order.
A sample of this file can be generated using:
tax.data <- read.table(header=F, con <- textConnection('
G9SS7BA01D15EC Bacteria(100) Cyanobacteria(84) unclassified
G9SS7BA01C9UIR Bacteria(100) Proteobacteria(94)
Alphaproteobacteria(89)
G9SS7BA01CM00D Bacteria(100) Proteobacteria(99)
Alphaproteobacteria(99)
'))
close(con)
What I try to do is to remove the parenthesis and the number inside
(which could contain a decimal point)
I assumed that the following command would solve it, but instead I got
an error.
tax...
2011 Apr 06
1
Creating a symmetric contingency table from two vectors with different length of levels in R
...w can I create a symmetric contingency table from two categorical vectors
having different length of levels?
For example one vector has 98 levels
TotalData1$Taxa.1
[1] "Aconoidasida" "Actinobacteria (class)"
"Actinopterygii" "Alphaproteobacteria"
[5] "Amoebozoa" "Amphibia"
"Anthozoa" "Aquificae (class)"
and so on .........
98 Levels: Aconoidasida Actinobacteria (class) ....
and the other vector has 105 levels
TotalData1$Taxa.2
[1] Flavobacte...
2010 Oct 28
1
Heatmap construction problems
....0,0.0,0.0,0.0,0.0,0.0
Firmicutes,1.0,7.6,8.3,31.9,2.1,6.9
Gemmatimonadetes,5.0,0.3,0.3,0.0,0.1,0.0
GN02,0.0,0.0,0.0,0.0,0.0,0.5
Nitrospirae,0.0,0.2,1.1,0.0,0.0,0.0
NKB19,0.0,0.0,0.9,0.0,0.0,0.0
OP8,0.0,0.1,0.0,0.0,0.0,0.0
OP10,0.6,0.2,0.5,0.0,0.6,0.6
Planctomycetes,0.9,0.5,6.5,2.2,2.0,2.3
Alphaproteobacteria,7.8,10.7,21.8,12.2,5.3,26.8
Betaproteobacteria,9.9,2.8,8.9,21.7,8.3,21.9
Deltaproteobacteria,0.5,0.2,1.8,2.0,1.2,7.1
Epsilonproteobacteria,0.0,0.0,0.0,0.1,0.0,0.2
Gammaproteobacteria,4.0,2.5,8.0,9.4,24.7,5.4
SC4,0.0,0.0,0.0,0.0,0.7,0.0
SM2F11,0.0,0.0,0.0,0.0,0.2,0.0
SPAM,0.0,0.1,0.0,0.0,0.1,...
2013 Mar 19
1
write random sampling as table output
...ermi WPS-2 ZB3 AD3 Elusimicrobia GAL15 ABY1_OD1 OP9 Fusobacteria HDBW-WB69 OP11 WS1 SR1 ZB2 AC1 OP3 OP8 NC10 NKB19 TM7 WS3 Gemmatimonadetes Lentisphaerae GN02 Armatimonadetes Tenericutes Spirochaetes Epsilonproteobacteria TM6 Acidobacteria Chlorobi Firmicutes Nitrospirae Chloroflexi Verrucomicrobia Alphaproteobacteria Betaproteobacteria Deltaproteobacteria Gammaproteobacteria uncl.Proteobacteria Actinobacteria Bacteroidetes Cyanobacteria Planctomycetes unclassified
Gi10Sep12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.002583979 0 0.004306632 0 0 0 0 0 0.001722653 0.000861326 0.004306632 0.006890612 0...