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annotate mixomics_blocksplsda_additional_funct.R @ 5:88c1fd2ac110 draft default tip

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents c8533e9298e5
children
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c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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1 #' @title Determination of selected variables for all components
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2 #' @description The function unionSelectBlockVariables determines, for each block, the selected block variables
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3 #' for all components.
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4 #' @param res_block_splsda type : sgccda. This parameter is the output of block.splsda function
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5 #' mixOmics.
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6 #' @details For each block, the function unionSelectBlockVariables returns 1 if the block variable is selected for
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7 #' at least one component. Otherwise, this function returns 0.
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8 #' @return type : list of matrix. For each block, if the block variable is selected, the value 1 is associated with
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9 #' this block variable. Otherwise the value 0 is associated with this block variable.
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10 #' @examples
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11 #' data(res_data_integration)
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12 #' list_union_selected_block_variables = unionSelectBlockVariables(res_data_integration)
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13 #' @export
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14 unionSelectBlockVariables <-function(res_block_splsda)
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15 {
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16 ncomp = res_block_splsda$ncomp[1]
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18 names_blocks = names(res_block_splsda$loadings)
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19 index_Y = which(names_blocks == "Y")
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20 names_blocks = names_blocks[ - index_Y]
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21 list_select_block_variables = list()
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23 for(i in 1:length(names_blocks))
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24 {
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25 mat_loadings_i = res_block_splsda$loadings[[i]]
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26 index_i = c()
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28 for(j in 1:ncomp)
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29 {
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30 loadings_i_j = mat_loadings_i[, j]
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31 index_i_j = which(loadings_i_j != 0)
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33 index_i = c(index_i, index_i_j)
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35 } # End for(j 1:ncomp).
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37 index_i = unique(index_i)
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39 mat_select_block_variables = matrix(0,
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40 nrow = dim(mat_loadings_i)[1],
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41 ncol = 1)
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42 mat_select_block_variables[index_i, 1] = rep(1, length(index_i))
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43 rownames(mat_select_block_variables) = rownames(mat_loadings_i)
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45 list_select_block_variables[[i]] = mat_select_block_variables
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47 } # End for(i in 1:length(names_blocks)).
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49 names(list_select_block_variables) = names_blocks
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51 return(list_select_block_variables)
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52 }