Rename liger package as rliger

Incorporated the modifications made during the development of rliger for CRAN submission

DESCRIPTION

@@ -1,10 +1,29 @@
-Package: liger
+Package: rliger
 Version: 0.5.0
-Date: 2021-01-11
+Date: 2021-01-18
 Type: Package
 Title: Linked Inference of Genomic Experimental Relationships
 Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
-Author: Joshua Welch, Chao Gao, Jialin Liu, Joshua Sodicoff
+Authors@R: c(
+  person(given = 'Joshua', family = 'Welch', email = 'welchjd@umich.edu', role = c('aut', 'ctb')),
+  person(given = 'Chao', family = 'Gao', email = 'gchao@umich.edu', role = c('aut', 'ctb', 'cre')),
+  person(given = 'Jialin', family = 'Liu', email = 'alanliu@umich.edu', role = c('aut', 'ctb')),
+  person(given = 'Joshua', family = 'Sodicoff', email = 'sodicoff@umich.edu', role = c('aut', 'ctb')),
+  person(given = 'Velina', family = 'Kozareva', role = c('aut', 'ctb')),
+  person(given = 'Evan', family = 'Macosko', role = c('aut', 'ctb')),
+  person(given = 'Paul', family = 'Hoffman', role = 'ctb'),
+  person(given = 'Ilya', family = 'Korsunsky', role = 'ctb'),
+  person(given = 'Robert', family = 'Lee', role = 'ctb')
+  )
+Author: Joshua Welch [aut, ctb], 
+        Chao Gao [aut, ctb, cre], 
+        Jialin Liu [aut, ctb], 
+        Joshua Sodicoff [aut, ctb],
+        Velina Kozareva [aut, ctb],
+        Evan Macosko [aut, ctb],
+        Paul Hoffman [ctb],
+        Ilya Korsunsky [ctb],
+        Robert Lee [ctb]
 Maintainer: Chao Gao <gchao@umich.edu>
 BugReports: https://github.com/welch-lab/liger/issues
 URL: https://github.com/welch-lab/liger
@@ -53,6 +72,5 @@ Suggests:
     org.Hs.eg.db,
     reactome.db,
     fgsea,
-    AnnotationDbi,
-    kBET
+    AnnotationDbi
 VignetteBuilder: knitr

NAMESPACE

@@ -4,13 +4,11 @@ S3method(optimizeALS,liger)
 S3method(optimizeALS,list)
 S3method(quantile_norm,liger)
 S3method(quantile_norm,list)
-export(Matrix.column_norm)
 export(calcARI)
 export(calcAgreement)
 export(calcAlignment)
 export(calcAlignmentPerCluster)
 export(calcDatasetSpecificity)
-export(calcGeneVars)
 export(calcPurity)
 export(convertOldLiger)
 export(createLiger)
@@ -61,8 +59,9 @@ export(suggestK)
 export(suggestLambda)
 exportClasses(liger)
 import(Matrix)
-import(doSNOW)
+import(doParallel)
 import(hdf5r)
+import(parallel)
 import(patchwork)
 importFrom(FNN,get.knn)
 importFrom(FNN,get.knnx)
@@ -147,8 +146,6 @@ importFrom(plyr,rbind.fill.matrix)
 importFrom(riverplot,makeRiver)
 importFrom(riverplot,riverplot)
 importFrom(rlang,.data)
-importFrom(snow,makeCluster)
-importFrom(snow,stopCluster)
 importFrom(stats,approxfun)
 importFrom(stats,complete.cases)
 importFrom(stats,heatmap)
@@ -170,4 +167,4 @@ importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
-useDynLib(liger)
+useDynLib(rliger)

R/RcppExports.R

@@ -2,67 +2,67 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 RunModularityClusteringCpp <- function(SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename) {
-    .Call('_liger_RunModularityClusteringCpp', PACKAGE = 'liger', SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename)
+    .Call('_rliger_RunModularityClusteringCpp', PACKAGE = 'rliger', SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename)
 }
 
 scaleNotCenterFast <- function(x) {
-    .Call('_liger_scaleNotCenterFast', PACKAGE = 'liger', x)
+    .Call('_rliger_scaleNotCenterFast', PACKAGE = 'rliger', x)
 }
 
 rowMeansFast <- function(x) {
-    .Call('_liger_rowMeansFast', PACKAGE = 'liger', x)
+    .Call('_rliger_rowMeansFast', PACKAGE = 'rliger', x)
 }
 
 rowVarsFast <- function(x, means) {
-    .Call('_liger_rowVarsFast', PACKAGE = 'liger', x, means)
+    .Call('_rliger_rowVarsFast', PACKAGE = 'rliger', x, means)
 }
 
 sumSquaredDeviations <- function(x, means) {
-    .Call('_liger_sumSquaredDeviations', PACKAGE = 'liger', x, means)
+    .Call('_rliger_sumSquaredDeviations', PACKAGE = 'rliger', x, means)
 }
 
 cpp_sumGroups_dgc <- function(x, p, i, ncol, groups, ngroups) {
-    .Call('_liger_cpp_sumGroups_dgc', PACKAGE = 'liger', x, p, i, ncol, groups, ngroups)
+    .Call('_rliger_cpp_sumGroups_dgc', PACKAGE = 'rliger', x, p, i, ncol, groups, ngroups)
 }
 
 cpp_sumGroups_dgc_T <- function(x, p, i, ncol, nrow, groups, ngroups) {
-    .Call('_liger_cpp_sumGroups_dgc_T', PACKAGE = 'liger', x, p, i, ncol, nrow, groups, ngroups)
+    .Call('_rliger_cpp_sumGroups_dgc_T', PACKAGE = 'rliger', x, p, i, ncol, nrow, groups, ngroups)
 }
 
 cpp_sumGroups_dense <- function(X, groups, ngroups) {
-    .Call('_liger_cpp_sumGroups_dense', PACKAGE = 'liger', X, groups, ngroups)
+    .Call('_rliger_cpp_sumGroups_dense', PACKAGE = 'rliger', X, groups, ngroups)
 }
 
 cpp_sumGroups_dense_T <- function(X, groups, ngroups) {
-    .Call('_liger_cpp_sumGroups_dense_T', PACKAGE = 'liger', X, groups, ngroups)
+    .Call('_rliger_cpp_sumGroups_dense_T', PACKAGE = 'rliger', X, groups, ngroups)
 }
 
 cpp_nnzeroGroups_dense <- function(X, groups, ngroups) {
-    .Call('_liger_cpp_nnzeroGroups_dense', PACKAGE = 'liger', X, groups, ngroups)
+    .Call('_rliger_cpp_nnzeroGroups_dense', PACKAGE = 'rliger', X, groups, ngroups)
 }
 
 cpp_nnzeroGroups_dense_T <- function(X, groups, ngroups) {
-    .Call('_liger_cpp_nnzeroGroups_dense_T', PACKAGE = 'liger', X, groups, ngroups)
+    .Call('_rliger_cpp_nnzeroGroups_dense_T', PACKAGE = 'rliger', X, groups, ngroups)
 }
 
 cpp_nnzeroGroups_dgc <- function(p, i, ncol, groups, ngroups) {
-    .Call('_liger_cpp_nnzeroGroups_dgc', PACKAGE = 'liger', p, i, ncol, groups, ngroups)
+    .Call('_rliger_cpp_nnzeroGroups_dgc', PACKAGE = 'rliger', p, i, ncol, groups, ngroups)
 }
 
 cpp_in_place_rank_mean <- function(v_temp, idx_begin, idx_end) {
-    .Call('_liger_cpp_in_place_rank_mean', PACKAGE = 'liger', v_temp, idx_begin, idx_end)
+    .Call('_rliger_cpp_in_place_rank_mean', PACKAGE = 'rliger', v_temp, idx_begin, idx_end)
 }
 
 cpp_rank_matrix_dgc <- function(x, p, nrow, ncol) {
-    .Call('_liger_cpp_rank_matrix_dgc', PACKAGE = 'liger', x, p, nrow, ncol)
+    .Call('_rliger_cpp_rank_matrix_dgc', PACKAGE = 'rliger', x, p, nrow, ncol)
 }
 
 cpp_rank_matrix_dense <- function(X) {
-    .Call('_liger_cpp_rank_matrix_dense', PACKAGE = 'liger', X)
+    .Call('_rliger_cpp_rank_matrix_dense', PACKAGE = 'rliger', X)
 }
 
 cpp_nnzeroGroups_dgc_T <- function(p, i, ncol, nrow, groups, ngroups) {
-    .Call('_liger_cpp_nnzeroGroups_dgc_T', PACKAGE = 'liger', p, i, ncol, nrow, groups, ngroups)
+    .Call('_rliger_cpp_nnzeroGroups_dgc_T', PACKAGE = 'rliger', p, i, ncol, nrow, groups, ngroups)
 }
 
 #' Fast calculation of feature count matrix
@@ -80,34 +80,34 @@ cpp_nnzeroGroups_dgc_T <- function(p, i, ncol, nrow, groups, ngroups) {
 #' samnple <- gene.counts + promoter.counts
 #' }
 makeFeatureMatrix <- function(bedmat, barcodes) {
-    .Call('_liger_makeFeatureMatrix', PACKAGE = 'liger', bedmat, barcodes)
+    .Call('_rliger_makeFeatureMatrix', PACKAGE = 'rliger', bedmat, barcodes)
 }
 
 cluster_vote <- function(nn_ranked, clusts) {
-    .Call('_liger_cluster_vote', PACKAGE = 'liger', nn_ranked, clusts)
+    .Call('_rliger_cluster_vote', PACKAGE = 'rliger', nn_ranked, clusts)
 }
 
 scale_columns_fast <- function(mat, scale = TRUE, center = TRUE) {
-    .Call('_liger_scale_columns_fast', PACKAGE = 'liger', mat, scale, center)
+    .Call('_rliger_scale_columns_fast', PACKAGE = 'rliger', mat, scale, center)
 }
 
 max_factor <- function(H, dims_use, center_cols = FALSE) {
-    .Call('_liger_max_factor', PACKAGE = 'liger', H, dims_use, center_cols)
+    .Call('_rliger_max_factor', PACKAGE = 'rliger', H, dims_use, center_cols)
 }
 
 solveNNLS <- function(C, B) {
-    .Call('_liger_solveNNLS', PACKAGE = 'liger', C, B)
+    .Call('_rliger_solveNNLS', PACKAGE = 'rliger', C, B)
 }
 
 ComputeSNN <- function(nn_ranked, prune) {
-    .Call('_liger_ComputeSNN', PACKAGE = 'liger', nn_ranked, prune)
+    .Call('_rliger_ComputeSNN', PACKAGE = 'rliger', nn_ranked, prune)
 }
 
 WriteEdgeFile <- function(snn, filename, display_progress) {
-    invisible(.Call('_liger_WriteEdgeFile', PACKAGE = 'liger', snn, filename, display_progress))
+    invisible(.Call('_rliger_WriteEdgeFile', PACKAGE = 'rliger', snn, filename, display_progress))
 }
 
 DirectSNNToFile <- function(nn_ranked, prune, display_progress, filename) {
-    .Call('_liger_DirectSNNToFile', PACKAGE = 'liger', nn_ranked, prune, display_progress, filename)
+    .Call('_rliger_DirectSNNToFile', PACKAGE = 'rliger', nn_ranked, prune, display_progress, filename)
 }