version 0.2.1

cran · Aug 8, 2015 · 181acc8 · 181acc8
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commit 181acc8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: slfm
 Type: Package
 Title: Tools for Fitting Sparse Latent Factor Model
-Version: 0.2.0
+Version: 0.2.1
 Author: Joao Duarte and Vinicius Mayrink
 Maintainer: Joao Duarte <jdanielnd@gmail.com>
 Description: Set of tools to find coherent patterns in microarray data
@@ -21,6 +21,6 @@ Imports: Rcpp (>= 0.11.0), coda, lattice
 LinkingTo: Rcpp, RcppArmadillo
 License: GPL-2
 NeedsCompilation: yes
-Packaged: 2015-07-29 00:03:10 UTC; jdanielnd
+Packaged: 2015-08-08 15:03:06 UTC; jdanielnd
 Repository: CRAN
-Date/Publication: 2015-07-29 06:21:43
+Date/Publication: 2015-08-08 17:41:43
diff --git a/MD5 b/MD5
@@ -1,13 +1,13 @@
-09c6391016c6b753e69a7534e10b8727 *DESCRIPTION
+c63be246b93827f2e4574d3231acab25 *DESCRIPTION
 87b17ef5c347ec4ca6d1641066700c30 *NAMESPACE
-bd3d6f4d64ee1b4f4804ad427a2745d2 *NEWS
+c16341d14e28876570e5c0f0a6b1ff87 *NEWS
 3e11a37d28ca0244100992886a82d3d5 *R/RcppExports.R
-c2bee89222b5b1d2f8a3b4ee0d5c59a6 *R/class_interval.r
+32e909834a9fc4e509216e033d45c8f6 *R/class_interval.r
 baabf72d4bc884b4c1a64efa0ab6929f *R/plot_matrix.r
 87f7eeceee7273541541ba5c589103ec *R/process_matrix.r
 43023f17cf4534c205f467c51594dff3 *R/slfm-package.r
-75aa158541ee3aed3c5084841a138dbc *R/slfm.r
-ccb2e56a2738d8fd42b70f0bf0adc061 *R/slfm_list.r
+ccef8b309606ef4d17db2c21c47019ea *R/slfm.r
+58005212f9aba9f2f545e0f1a0630f3e *R/slfm_list.r
 540f05f21a09f459cc33f9d244ac919d *man/plot_matrix.Rd
 59958c4ef88f62f062a57ede17dd64c7 *man/process_matrix.Rd
 50feb9e98613c1d6ee4e2ca0aa62a5fd *man/slfm-package.Rd

diff --git a/NEWS b/NEWS
@@ -1,3 +1,10 @@
+slfm 0.2.1
+===========
+
+* adding % significant column to slfm_list output
+
+* using S/N/I notation to slfm output
+
 slfm 0.2.0
 ===========
 

diff --git a/R/class_interval.r b/R/class_interval.r
@@ -1,10 +1,10 @@
 class_interval_uni <- function(x, cv = 0.5) {
     if(x[2] < cv) {
-        clas <- "A"
+        clas <- "N"
     } else if(x[1] > cv) {
-        clas <- "P"
+        clas <- "S"
     } else {
-        clas <- "M"
+        clas <- "I"
     }
     return(clas)
 }
@@ -16,9 +16,9 @@ class_interval <- function(x) {
 format_classification <- function(x) {
   x <- as.factor(x)
   lvls <- levels(x)
-  lvls[lvls == "P"] <- "Present"
-  lvls[lvls == "M"] <- "Marginal"
-  lvls[lvls == "A"] <- "Absent"
+  lvls[lvls == "S"] <- "S"
+  lvls[lvls == "I"] <- "I"
+  lvls[lvls == "N"] <- "N"
   levels(x) <- lvls
   x
 }

diff --git a/R/slfm.r b/R/slfm.r
@@ -81,10 +81,10 @@ slfm <- function(
     x = x,
     alpha = table_alpha,
     lambda = table_lambda,
-    sigma = table_sigma,
+    sigma2 = table_sigma,
     alpha_matrix = alpha_matrix,
     lambda_matrix = lambda_matrix,
-    sigma_matrix = sigma_matrix,
+    sigma2_matrix = sigma_matrix,
     q_star = q_star_matrix,
     z_matrix = z_matrix,
     classification = alpha_clas)

diff --git a/R/slfm_list.r b/R/slfm_list.r
@@ -29,21 +29,26 @@ slfm_list <- function(
   files_list <- list.files(path, recursive = recursive, full.names = T)
 
   message("* |Press Ctrl + C to cancel...")
-  pb <- txtProgressBar(0, length(files_list), style = 3, title = "BLA")
+  pb <- txtProgressBar(0, length(files_list), style = 3, title = "")
+
+  MATRIX_CLASSIFICATION <- c("Present", "Marginal", "Absent")
+  names(MATRIX_CLASSIFICATION) <- c("S", "I", "N")
 
   results_list <- list()
   for(i in 1:length(files_list)) {
     file_name <- files_list[i]
     mat <- read.table(file_name)
 
     res <- slfm(mat, a, b, gamma_a, gamma_b, omega_0, omega_1, sample, burnin, lag, degenerate)
-    final_clas <- names(which.max(table(res$classification)))
-    results_list[[i]] <- c(name=basename(tools::file_path_sans_ext(file_name)), clas=final_clas)
+    clas_table <- table(res$classification)
+    final_clas <- MATRIX_CLASSIFICATION[names(which.max(clas_table))]
+    freq <- format(round(clas_table["S"]/sum(clas_table), 4), nsmall = 4)
+    results_list[[i]] <- c(name = basename(tools::file_path_sans_ext(file_name)), clas = final_clas, frequency = freq)
 
     setTxtProgressBar(pb, i)
   }
   close(pb)
   ret <- as.data.frame(do.call(rbind, results_list))
-  names(ret) <- c("File", "Classification")
+  names(ret) <- c("File", "Classification", "Significant %")
   ret
 }