matchBox (version 1.14.0)

matchBox-package: 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;

References

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