Clean init for presto

Package: presto

Title: Fast Functions for Differential Expression using Wilcox and AUC

biocViews: StatisticalMethod, DifferentialExpression, GeneExpression, RNASeq, SingleCell

Version: 0.99.0

Authors@R: c(

    person("Ilya", "Korsunsky", email = "ilya.korsunsky@gmail.com", 

        role = c("cre", "aut"), comment = c(ORCID = "0000-0003-4848-3948")),

    person("Aparna", "Nathan", 

        role = "aut"),

    person("Nghia", "Millard", 

        role = "aut", comment = c(ORCID = "0000-0002-0518-7674")),

    person("Soumya", "Raychaudhuri", 

        role = c("aut"), comment = c(ORCID = "0000-0002-1901-8265"))

    )

Description: Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment. 

License: GPL-3 + file LICENSE

Encoding: UTF-8

Depends: Rcpp

LinkingTo: Rcpp, RcppArmadillo

Imports: 

    dplyr, 

    methods,

    tidyr, 

    reshape2

RoxygenNote: 6.1.1

Suggests: 

    knitr,

    rmarkdown,

    testthat,

    Seurat,

    SingleCellExperiment, 

    SummarizedExperiment,

    broom,

    BiocStyle

VignetteBuilder: knitr

# Generated by roxygen2: do not edit by hand

S3method(nnzeroGroups,dgCMatrix)

S3method(nnzeroGroups,matrix)

S3method(rank_matrix,dgCMatrix)

S3method(rank_matrix,matrix)

S3method(sumGroups,dgCMatrix)

S3method(sumGroups,matrix)

S3method(wilcoxauc,Seurat)

S3method(wilcoxauc,SingleCellExperiment)

S3method(wilcoxauc,default)

S3method(wilcoxauc,seurat)

export("%>%")

export(nnzeroGroups)

export(rank_matrix)

export(sumGroups)

export(top_markers)

export(wilcoxauc)

import(Rcpp)

importClassesFrom(Matrix,TsparseMatrix)

importClassesFrom(Matrix,dgCMatrix)

importClassesFrom(Matrix,dgTMatrix)

importClassesFrom(Matrix,dgeMatrix)

importFrom(Matrix,Matrix)

importFrom(Rcpp,evalCpp)

importFrom(Rcpp,loadModule)

importFrom(Rcpp,sourceCpp)

importFrom(dplyr,"%>%")

importFrom(methods,as)

importFrom(methods,is)

importFrom(rlang,.data)

importFrom(stats,p.adjust)

importFrom(stats,pnorm)

importFrom(stats,wilcox.test)

importFrom(utils,head)

useDynLib(presto)

# presto 0.99.0

Initial submission.

# Generated by using Rcpp::compileAttributes() -> do not edit by hand

# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

cpp_sumGroups_dgc <- function(x, p, i, ncol, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dgc', PACKAGE = 'presto', x, p, i, ncol, groups, ngroups)

}

cpp_sumGroups_dgc_T <- function(x, p, i, ncol, nrow, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dgc_T', PACKAGE = 'presto', x, p, i, ncol, nrow, groups, ngroups)

}

cpp_sumGroups_dense <- function(X, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dense', PACKAGE = 'presto', X, groups, ngroups)

}

cpp_sumGroups_dense_T <- function(X, groups, ngroups) {

    .Call('_presto_cpp_sumGroups_dense_T', PACKAGE = 'presto', X, groups, ngroups)

}

cpp_nnzeroGroups_dense <- function(X, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dense', PACKAGE = 'presto', X, groups, ngroups)

}

cpp_nnzeroGroups_dense_T <- function(X, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dense_T', PACKAGE = 'presto', X, groups, ngroups)

}

cpp_nnzeroGroups_dgc <- function(p, i, ncol, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dgc', PACKAGE = 'presto', p, i, ncol, groups, ngroups)

}

cpp_in_place_rank_mean <- function(v_temp, idx_begin, idx_end) {

    .Call('_presto_cpp_in_place_rank_mean', PACKAGE = 'presto', v_temp, idx_begin, idx_end)

}

cpp_rank_matrix_dgc <- function(x, p, nrow, ncol) {

    .Call('_presto_cpp_rank_matrix_dgc', PACKAGE = 'presto', x, p, nrow, ncol)

}

cpp_rank_matrix_dense <- function(X) {

    .Call('_presto_cpp_rank_matrix_dense', PACKAGE = 'presto', X)

}

cpp_nnzeroGroups_dgc_T <- function(p, i, ncol, nrow, groups, ngroups) {

    .Call('_presto_cpp_nnzeroGroups_dgc_T', PACKAGE = 'presto', p, i, ncol, nrow, groups, ngroups)

}