R: A package to produce Correspondence-At-Top plots (CAT-plots)...
matchBox-package
R Documentation
A package to produce Correspondence-At-Top plots (CAT-plots) between ranked list of genes.
Description
The matchBox package allows to annotate and compare
ranked vectors (e.g. by differential expression) of genomic features
(e.g. genes, or probe sets), using CAT curves.
A CAT curve displays the overlap proportion between two ranked
vectors of identifiers against the number of considered features.
This techiques was used for comparing differential gene expression
results obtained from different platforms in different laboratories
(see Irizarry et al, Nat Methods (2005))
matchBox package features
Enables to filter data.frames containing feature
identifiers and ranking statistics;
Enables to identify the common set of features across
results from different genomic experiments;
Enables to merge multiple data.frames based on
the commons set of features;
Computes the overlap proportion between any pair of ranked
features;
Creates plots of the proportion of overlap along
with conidence intervals;
Irizarry, R. A.; Warren, D.; Spencer, F.; Kim, I. F.; Biswal, S.;
Frank, B. C.; Gabrielson, E.; Garcia, J. G. N.; Geoghegan, J.;
Germino, G.; Griffin, C.; Hilmer, S. C.; Hoffman, E.;
Jedlicka, A. E.; Kawasaki, E.; Martinez-Murillo, F.;
Morsberger, L.; Lee, H.; Petersen, D.; Quackenbush, J.;
Scott, A.; Wilson, M.; Yang, Y.; Ye, S. Q.
and Yu, W. Multiple-laboratory comparison of microarray platforms.
Nat Methods, 2005, 2, 345-350
Ross, A. E.; Marchionni, L.; Vuica-Ross, M.; Cheadle, C.;
Fan, J.; Berman, D. M.; and Schaeffer E. M.
Gene Expression Pathways of High Grade Localized Prostate Cancer.
Prostate 2011, 71, 1568-1578
Benassi, B.; Flavin, R.; Marchionni, L.; Zanata, S.; Pan, Y.;
Chowdhury, D.; Marani, M.; Strano, S.; Muti, P.; and Blandino, G.
c-Myc is activated via USP2a-mediated modulation of microRNAs
in prostate cancer. Cancer Discovery, 2012, March, 2, 236-247