Mercurial > repos > ppericard > viscorvar
diff mixomics_blocksplsda_additional_funct.R @ 2:c8533e9298e5 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author | ppericard |
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date | Fri, 23 Oct 2020 10:15:56 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda_additional_funct.R Fri Oct 23 10:15:56 2020 +0000 @@ -0,0 +1,52 @@ +#' @title Determination of selected variables for all components +#' @description The function unionSelectBlockVariables determines, for each block, the selected block variables +#' for all components. +#' @param res_block_splsda type : sgccda. This parameter is the output of block.splsda function +#' mixOmics. +#' @details For each block, the function unionSelectBlockVariables returns 1 if the block variable is selected for +#' at least one component. Otherwise, this function returns 0. +#' @return type : list of matrix. For each block, if the block variable is selected, the value 1 is associated with +#' this block variable. Otherwise the value 0 is associated with this block variable. +#' @examples +#' data(res_data_integration) +#' list_union_selected_block_variables = unionSelectBlockVariables(res_data_integration) +#' @export +unionSelectBlockVariables <-function(res_block_splsda) +{ + ncomp = res_block_splsda$ncomp[1] + + names_blocks = names(res_block_splsda$loadings) + index_Y = which(names_blocks == "Y") + names_blocks = names_blocks[ - index_Y] + list_select_block_variables = list() + + for(i in 1:length(names_blocks)) + { + mat_loadings_i = res_block_splsda$loadings[[i]] + index_i = c() + + for(j in 1:ncomp) + { + loadings_i_j = mat_loadings_i[, j] + index_i_j = which(loadings_i_j != 0) + + index_i = c(index_i, index_i_j) + + } # End for(j 1:ncomp). + + index_i = unique(index_i) + + mat_select_block_variables = matrix(0, + nrow = dim(mat_loadings_i)[1], + ncol = 1) + mat_select_block_variables[index_i, 1] = rep(1, length(index_i)) + rownames(mat_select_block_variables) = rownames(mat_loadings_i) + + list_select_block_variables[[i]] = mat_select_block_variables + + } # End for(i in 1:length(names_blocks)). + + names(list_select_block_variables) = names_blocks + + return(list_select_block_variables) +}