| Title: | Data for Combination Connectivity Mapping (ccmap) Package |
|---|---|
| Description: | This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. |
| Authors: | Alex Pickering |
| Maintainer: | Alex Pickering <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.39.1 |
| Built: | 2026-10-13 14:23:52 UTC |
| Source: | https://git.bioconductor.org/packages/ccdata |
Moderated unbiased effect sizes values for all 1309 drugs in the Connectivity Map build 02.
data(cmap_es)data(cmap_es)
An object of class matrix with 13832 rows and 1309 columns.
Calculated as described by Marot et al (see reference) using toptable
from limma and effectsize from metaMA.
A matrix where columns correspond to drugs and rows to gene symbols.
Marot G, Foulley JL, Mayer CD, Jaffrézic F. Moderated effect size and P-value combinations for microarray meta-analyses. Bioinformatics. 2009 Oct 15;25(20):2692-9. doi: 10.1093/bioinformatics/btp444.
Variances of unbiased effect sizes values for all 1309 drugs in the Connectivity Map build 02.
data(cmap_var)data(cmap_var)
An object of class matrix with 13832 rows and 1309 columns.
Calculated as described by Marot et al (see reference) using toptable
from limma and effectsize from metaMA.
A matrix where columns correspond to drugs and rows to gene symbols.
Marot G, Foulley JL, Mayer CD, Jaffrézic F. Moderated effect size and P-value combinations for microarray meta-analyses. Bioinformatics. 2009 Oct 15;25(20):2692-9. doi: 10.1093/bioinformatics/btp444.
Order is as required for input and produced by output of net1/net2 predictions.
data(genes)data(genes)
An object of class character of length 11525.
A character vector of 11525 HGNC symbols.
Moderated unbiased effect sizes values for all 230829 LINCS l1000 signatures.
data(l1000_es)data(l1000_es)
An object of class matrix with 1001 rows and 230829 columns.
Calculated as described by Marot et al (see reference) using toptable
from limma and effectsize from metaMA.
A matrix where columns correspond to perturbagens and rows to gene symbols.
Marot G, Foulley JL, Mayer CD, Jaffrézic F. Moderated effect size and P-value combinations for microarray meta-analyses. Bioinformatics. 2009 Oct 15;25(20):2692-9. doi: 10.1093/bioinformatics/btp444.
Contains weight matrices and bias vectors needed to make predictions.
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An object of class list of length 4.
List with matrices W1/W2 and vectors b1/b2.
Contains weight matrices and bias vectors needed to make predictions.
#NA#NA
An object of class list of length 4.
List with matrices W1/W2 and vectors b1/b2.
Model stacks predictions from net1 and net2 with effect size values from cmap_es and variance values from cmap_var.
#NA#NA
An object of class xgb.Booster of length 2.
Object of class xgb.Booster