compare_sorted_geneSets {scsR} | R Documentation |
This method can be used to compare the performances of two different sorted gene vectors (A1 and A2) relative to a reference vector (B). To perform the comparison we use n best hits from genesetA1 and genesetA2. n is defined as the number of elements of the smallest of the two vectors(after intersecting it with the background). For the comparison see also the enrichment_geneSet method.
compare_sorted_geneSets(genesetA1, genesetA2, genesetB, background, limA=NULL, limB=NULL)
genesetA1 |
vector of sorted genes (character vector) |
genesetA2 |
vector of sorted genes (character vector) |
genesetB |
vector of genes to be used as reference (character vector) |
background |
vector of genes to be used as background (character vector) |
limA |
limit the number of genes of the vector genesetA1 to the first limA genes (integer) |
limB |
limit the number of genes of the vector genesetB1 to the first limB genes (integer) |
Andrea Franceschini
data(uuk_screen) data(uuk_screen_dh) compare_sorted_geneSets(unique(uuk_screen$GeneID)[1:200], unique(arrange(add_rank_col(uuk_screen), log_pval_rsa)$GeneID)[1:200], unique(uuk_screen_dh$GeneID)[1:400], intersect(uuk_screen$GeneID, uuk_screen_dh$GeneID) )