Mercurial > repos > vandelj > giant_gsea_format

comparison src/utils.R @ 2:738ed1deed23 draft default tip

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit 89b7d0e8812f53222691cffe29bd48be6519829d"
author vandelj
date Fri, 25 Sep 2020 08:51:31 +0000
parents 3022feec50fe
children
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1:d72f1bc5ce9e 2:738ed1deed23
16 16
17 #extendedDist function to correlation measure 17 #extendedDist function to correlation measure
18 distExtended <- function(x,method) { 18 distExtended <- function(x,method) {
19 if(method %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"))return(dist(x,method = method)) 19 if(method %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"))return(dist(x,method = method))
20 if(method %in% c("pearson", "spearman", "kendall"))return(as.dist(1-cor(t(x),method=method))/2) 20 if(method %in% c("pearson", "spearman", "kendall"))return(as.dist(1-cor(t(x),method=method))/2)
21 if(method %in% c("absPearson", "absSpearman", "absKendall"))return(as.dist(1-abs(cor(t(x),method=method)))) 21 if(method %in% c("absPearson", "absSpearman", "absKendall"))return(as.dist(1-abs(cor(t(x),method=tolower(substr(method,4,15))))))
22 return(NULL) 22 return(NULL)
23 } 23 }
24 24
25 ##comment function to display message and optionnaly add it to log file 25 ##comment function to display message and optionnaly add it to log file
26 26