claudinLowData: claudinLowData for use in the claudinLow classifier. Data...
In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer
Description
Usage
Format
Source
References
See Also
Examples
Description
Training and Testing Data for use with the Claudin-Low Classifier
Usage
1
Format
claudinLowData is a dataset containing one list with six sublists:
- claudinLowData
xd: Matrix of 807 features and 52 samples. classes: factor to split samples. nfeatures: number of features. nsamples: number of samples. fnames: names of features. snames: names of samples.
Source
http://www.biomedcentral.com/content/pdf/bcr2635.pdf
References
Aleix Prat, Joel S Parker, Olga Karginova, Cheng Fan, Chad Livasy, Jason I Herschkowitz, Xiaping He, and Charles M. Perou (2010) "Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer", Breast Cancer Research, 12(5):R68
See Also
Examples
1
2
3
Example output
Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: impute
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:limma’:
plotMA
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
List of 6
$ xd : num [1:807, 1:52] -1.1 -4.06 -2.68 2.12 -2.69 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:807] "6712" "51599" "7022" "1969" ...
.. ..$ : chr [1:52] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin" "MDAMB157 || Claudin" ...
$ classes :'data.frame': 52 obs. of 1 variable:
..$ Group: Factor w/ 2 levels "Claudin","Others": 1 1 1 1 1 1 1 1 1 2 ...
.. ..- attr(*, "names")= chr [1:52] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin" "MDAMB157 || Claudin" ...
$ nfeatures: int 807
$ nsamples : int 52
$ fnames : chr [1:807] "6712" "51599" "7022" "1969" ...
$ snames : chr [1:52] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin" "MDAMB157 || Claudin" ...
$xd
BT549 || Claudin HBL100 || Claudin HS578T || Claudin MDAMB157 || Claudin
6712 -1.097 -0.131 -1.329 -1.299
51599 -4.057 -3.190 -4.428 -4.209
7022 -2.680 -2.743 -2.579 0.185
1969 2.121 1.576 2.125 1.273
79679 -2.686 -1.983 -1.927 -2.592
8611 2.198 0.884 0.307 2.234
MDAMB231 || Claudin MDAMB435 || Claudin MDAMB436 || Claudin
6712 -0.934 -1.516 -0.736
51599 -2.326 -4.207 -3.599
7022 -1.939 -0.145 -1.273
1969 3.247 -1.568 0.486
79679 -2.820 -2.828 -2.707
8611 0.013 0.400 0.412
SUM159PT || Claudin SUM1315 || Claudin 600MPE || Others AU565 || Others
6712 -0.576 -1.313 0.861 1.273
51599 -4.246 -5.552 2.369 -0.318
7022 -2.556 -3.455 -1.168 1.599
1969 2.425 1.219 0.174 0.197
79679 -3.377 -2.659 2.694 4.630
8611 1.902 2.623 -0.175 -0.690
BT20 || Others BT474 || Others BT483 || Others CAMA1 || Others
6712 -0.730 0.748 0.616 -0.139
51599 -0.237 1.565 -0.430 -0.084
7022 0.908 2.069 2.983 -0.547
1969 1.649 -1.730 -2.978 -2.148
79679 -3.262 -0.251 -1.667 2.718
8611 -1.529 -0.977 -0.139 -1.969
DU4475 || Others HCC38 || Others HCC70 || Others HCC202 || Others
6712 0.073 -0.263 0.202 1.581
51599 0.031 -1.499 1.857 2.003
7022 0.544 -1.201 -0.797 -1.462
1969 1.694 2.665 -0.063 0.390
79679 -1.316 0.178 3.014 3.098
8611 -0.543 1.780 0.408 -0.197
HCC1007 || Others HCC1008 || Others HCC1143 || Others HCC1187 || Others
6712 -0.571 2.279 -0.116 1.112
51599 -0.638 1.956 1.448 -0.417
7022 1.804 1.225 0.000 -1.269
1969 -0.164 -2.130 -0.868 -2.063
79679 2.462 2.705 2.453 1.754
8611 0.930 -0.611 0.187 -0.895
HCC1428 || Others HCC1500 || Others HCC1569 || Others HCC1599 || Others
6712 0.182 -0.922 -0.359 0.629
51599 0.940 1.470 -1.183 2.388
7022 3.124 -1.886 1.241 0.184
1969 -2.800 1.699 -0.888 -1.306
79679 3.689 -2.517 1.951 3.085
8611 -1.175 0.807 0.831 -0.134
HCC1937 || Others HCC1954 || Others HCC2157 || Others HCC2185 || Others
6712 0.750 -0.936 0.728 0.411
51599 2.049 2.159 2.254 0.006
7022 0.426 1.051 1.903 0.797
1969 0.359 3.427 -0.031 -0.062
79679 2.463 -0.831 4.702 2.122
8611 0.764 -0.312 -0.734 -0.930
HCC3153 || Others LY2 || Others MCF7 || Others MDAMB134 || Others
6712 0.264 0.979 0.380 -0.125
51599 2.142 -1.610 1.114 -0.532
7022 -0.387 -0.142 1.618 1.143
1969 -0.125 -1.512 -0.475 -1.992
79679 3.445 -3.000 -2.089 -2.154
8611 1.225 -0.764 0.490 0.369
MDAMB175 || Others MDAMB361 || Others MDAMB415 || Others
6712 0.486 0.318 -0.065
51599 0.111 -0.189 1.019
7022 0.359 -0.461 -2.106
1969 -1.984 -2.177 -1.845
79679 0.681 -0.979 1.685
8611 -0.090 -0.091 1.559
MDAMB453 || Others MDAMB468 || Others SKBR3 || Others SUM44PE || Others
6712 -0.958 -0.650 1.467 -0.235
51599 0.010 1.829 -0.127 -1.164
7022 -1.292 -0.138 2.414 0.414
1969 -1.765 0.454 -0.363 -1.571
79679 -1.961 4.886 4.994 2.766
8611 -1.147 -0.620 -1.085 1.509
SUM52PE || Others SUM149PT || Others SUM185PE || Others
6712 -0.231 -0.108 -0.737
51599 -2.999 0.876 0.953
7022 0.861 -0.327 0.302
1969 -1.353 2.054 0.379
79679 -2.668 -2.273 -0.838
8611 -0.998 -0.680 -0.393
SUM190PT || Others SUM225CWN || Others T47D || Others UACC812 || Others
6712 -0.222 0.941 1.373 0.215
51599 0.604 0.711 -0.880 0.391
7022 -0.882 -0.004 0.263 1.219
1969 1.815 1.026 -2.709 -1.792
79679 0.749 0.947 -1.578 2.745
8611 -0.098 0.455 0.996 -0.002
ZR751 || Others ZR7530 || Others ZR75B || Others
6712 0.387 0.342 -0.693
51599 -2.534 -1.577 -0.100
7022 -0.564 -0.236 0.239
1969 -2.650 -1.381 -2.082
79679 3.810 -2.184 0.326
8611 -1.014 0.298 -0.262
$classes
Group
BT549 || Claudin Claudin
HBL100 || Claudin Claudin
HS578T || Claudin Claudin
MDAMB157 || Claudin Claudin
MDAMB231 || Claudin Claudin
MDAMB435 || Claudin Claudin
$nfeatures
[1] 807
$nsamples
[1] 52
$fnames
[1] "6712" "51599" "7022" "1969" "79679" "8611"
$snames
[1] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin"
[4] "MDAMB157 || Claudin" "MDAMB231 || Claudin" "MDAMB435 || Claudin"
genefu documentation built on Jan. 28, 2021, 2:01 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Format Source References See Also Examples
Description
Training and Testing Data for use with the Claudin-Low Classifier
Usage
1 |
Format
claudinLowData is a dataset containing one list with six sublists:
- claudinLowData
xd: Matrix of 807 features and 52 samples. classes: factor to split samples. nfeatures: number of features. nsamples: number of samples. fnames: names of features. snames: names of samples.
Source
http://www.biomedcentral.com/content/pdf/bcr2635.pdf
References
Aleix Prat, Joel S Parker, Olga Karginova, Cheng Fan, Chad Livasy, Jason I Herschkowitz, Xiaping He, and Charles M. Perou (2010) "Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer", Breast Cancer Research, 12(5):R68
See Also
Examples
1 2 3 |
Example output
Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: impute
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:limma’:
plotMA
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
List of 6
$ xd : num [1:807, 1:52] -1.1 -4.06 -2.68 2.12 -2.69 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:807] "6712" "51599" "7022" "1969" ...
.. ..$ : chr [1:52] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin" "MDAMB157 || Claudin" ...
$ classes :'data.frame': 52 obs. of 1 variable:
..$ Group: Factor w/ 2 levels "Claudin","Others": 1 1 1 1 1 1 1 1 1 2 ...
.. ..- attr(*, "names")= chr [1:52] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin" "MDAMB157 || Claudin" ...
$ nfeatures: int 807
$ nsamples : int 52
$ fnames : chr [1:807] "6712" "51599" "7022" "1969" ...
$ snames : chr [1:52] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin" "MDAMB157 || Claudin" ...
$xd
BT549 || Claudin HBL100 || Claudin HS578T || Claudin MDAMB157 || Claudin
6712 -1.097 -0.131 -1.329 -1.299
51599 -4.057 -3.190 -4.428 -4.209
7022 -2.680 -2.743 -2.579 0.185
1969 2.121 1.576 2.125 1.273
79679 -2.686 -1.983 -1.927 -2.592
8611 2.198 0.884 0.307 2.234
MDAMB231 || Claudin MDAMB435 || Claudin MDAMB436 || Claudin
6712 -0.934 -1.516 -0.736
51599 -2.326 -4.207 -3.599
7022 -1.939 -0.145 -1.273
1969 3.247 -1.568 0.486
79679 -2.820 -2.828 -2.707
8611 0.013 0.400 0.412
SUM159PT || Claudin SUM1315 || Claudin 600MPE || Others AU565 || Others
6712 -0.576 -1.313 0.861 1.273
51599 -4.246 -5.552 2.369 -0.318
7022 -2.556 -3.455 -1.168 1.599
1969 2.425 1.219 0.174 0.197
79679 -3.377 -2.659 2.694 4.630
8611 1.902 2.623 -0.175 -0.690
BT20 || Others BT474 || Others BT483 || Others CAMA1 || Others
6712 -0.730 0.748 0.616 -0.139
51599 -0.237 1.565 -0.430 -0.084
7022 0.908 2.069 2.983 -0.547
1969 1.649 -1.730 -2.978 -2.148
79679 -3.262 -0.251 -1.667 2.718
8611 -1.529 -0.977 -0.139 -1.969
DU4475 || Others HCC38 || Others HCC70 || Others HCC202 || Others
6712 0.073 -0.263 0.202 1.581
51599 0.031 -1.499 1.857 2.003
7022 0.544 -1.201 -0.797 -1.462
1969 1.694 2.665 -0.063 0.390
79679 -1.316 0.178 3.014 3.098
8611 -0.543 1.780 0.408 -0.197
HCC1007 || Others HCC1008 || Others HCC1143 || Others HCC1187 || Others
6712 -0.571 2.279 -0.116 1.112
51599 -0.638 1.956 1.448 -0.417
7022 1.804 1.225 0.000 -1.269
1969 -0.164 -2.130 -0.868 -2.063
79679 2.462 2.705 2.453 1.754
8611 0.930 -0.611 0.187 -0.895
HCC1428 || Others HCC1500 || Others HCC1569 || Others HCC1599 || Others
6712 0.182 -0.922 -0.359 0.629
51599 0.940 1.470 -1.183 2.388
7022 3.124 -1.886 1.241 0.184
1969 -2.800 1.699 -0.888 -1.306
79679 3.689 -2.517 1.951 3.085
8611 -1.175 0.807 0.831 -0.134
HCC1937 || Others HCC1954 || Others HCC2157 || Others HCC2185 || Others
6712 0.750 -0.936 0.728 0.411
51599 2.049 2.159 2.254 0.006
7022 0.426 1.051 1.903 0.797
1969 0.359 3.427 -0.031 -0.062
79679 2.463 -0.831 4.702 2.122
8611 0.764 -0.312 -0.734 -0.930
HCC3153 || Others LY2 || Others MCF7 || Others MDAMB134 || Others
6712 0.264 0.979 0.380 -0.125
51599 2.142 -1.610 1.114 -0.532
7022 -0.387 -0.142 1.618 1.143
1969 -0.125 -1.512 -0.475 -1.992
79679 3.445 -3.000 -2.089 -2.154
8611 1.225 -0.764 0.490 0.369
MDAMB175 || Others MDAMB361 || Others MDAMB415 || Others
6712 0.486 0.318 -0.065
51599 0.111 -0.189 1.019
7022 0.359 -0.461 -2.106
1969 -1.984 -2.177 -1.845
79679 0.681 -0.979 1.685
8611 -0.090 -0.091 1.559
MDAMB453 || Others MDAMB468 || Others SKBR3 || Others SUM44PE || Others
6712 -0.958 -0.650 1.467 -0.235
51599 0.010 1.829 -0.127 -1.164
7022 -1.292 -0.138 2.414 0.414
1969 -1.765 0.454 -0.363 -1.571
79679 -1.961 4.886 4.994 2.766
8611 -1.147 -0.620 -1.085 1.509
SUM52PE || Others SUM149PT || Others SUM185PE || Others
6712 -0.231 -0.108 -0.737
51599 -2.999 0.876 0.953
7022 0.861 -0.327 0.302
1969 -1.353 2.054 0.379
79679 -2.668 -2.273 -0.838
8611 -0.998 -0.680 -0.393
SUM190PT || Others SUM225CWN || Others T47D || Others UACC812 || Others
6712 -0.222 0.941 1.373 0.215
51599 0.604 0.711 -0.880 0.391
7022 -0.882 -0.004 0.263 1.219
1969 1.815 1.026 -2.709 -1.792
79679 0.749 0.947 -1.578 2.745
8611 -0.098 0.455 0.996 -0.002
ZR751 || Others ZR7530 || Others ZR75B || Others
6712 0.387 0.342 -0.693
51599 -2.534 -1.577 -0.100
7022 -0.564 -0.236 0.239
1969 -2.650 -1.381 -2.082
79679 3.810 -2.184 0.326
8611 -1.014 0.298 -0.262
$classes
Group
BT549 || Claudin Claudin
HBL100 || Claudin Claudin
HS578T || Claudin Claudin
MDAMB157 || Claudin Claudin
MDAMB231 || Claudin Claudin
MDAMB435 || Claudin Claudin
$nfeatures
[1] 807
$nsamples
[1] 52
$fnames
[1] "6712" "51599" "7022" "1969" "79679" "8611"
$snames
[1] "BT549 || Claudin" "HBL100 || Claudin" "HS578T || Claudin"
[4] "MDAMB157 || Claudin" "MDAMB231 || Claudin" "MDAMB435 || Claudin"
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.