integrate_replicates {FindIT2} | R Documentation |
integrate value from replicates
integrate_replicates( mt, colData, fun = NULL, type = c("value", "rank", "rank_zscore", "pvalue") )
mt |
value matrix |
colData |
a data.frame with a single column named with "type". Rows of colData correspond to columns of mt. |
fun |
the function you want to use. If set NULL, program will decide integrate method according to your 'type' parameter. |
type |
one of 'value', 'rank', 'rank_zscore', pvalue'. value will use mean to integrate replicates, rank will use product, rank_zscore will use Stouffer's method and pvalue will use CCT(Cauchy distribution) |
matrix
mt <- matrix(runif(100, 0, 1), nrow = 10) colnames(mt) <- paste0(paste0("type", 1:5), "_", rep(1:2, 5)) rownames(mt) <- paste0("TF", 1:10) colData <- data.frame( type = gsub("_[0-9]", "", colnames(mt)), row.names = colnames(mt) ) integrate_replicates(mt, colData, type = "value")