diff --git a/DESCRIPTION b/DESCRIPTION index e25f297..c0e2018 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,14 +1,25 @@ Package: SPARK Type: Package Title: Spatial Pattern Recognition via Kernels -Version: 1.1.0 -Date: 2020-10-07 +Version: 1.1.1 +Date: 2021-02-02 Author: Shiquan Sun, Jiaqiang Zhu, and Xiang Zhou Maintainer: Jiaqiang Zhu Description: SPARK is an efficient tool for identifying spatial expression patterns. SPARK directly models raw count data generated from various spatial resolved transcriptomic techniques. With a new efficient penalized quasi-likelihood based algorithm, SPARK is scalable to data sets with tens of thousands of genes measured on thousands of samples. Build upon a non-parametric framework, SPARK-X is scalable to large-scale data sets with tens of thousands of genes measured on hundred thousands of samples. License: GPL-3 Depends: R (>= 3.4.0), methods -Imports: Rcpp (>= 1.0.5),foreach,doParallel,parallel,Matrix,CompQuadForm,matlab,pracma +Imports: + Rcpp (>= 1.0.5), + foreach, + doParallel, + parallel, + Matrix, + CompQuadForm, + matlab, + pracma, + doSNOW, + pbmcapply, + RcppArmadillo LinkingTo: Rcpp, RcppArmadillo NeedsCompilation: yes RoxygenNote: 7.1.1 diff --git a/NAMESPACE b/NAMESPACE index 626fbe3..a3e8fde 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -38,11 +38,11 @@ importFrom(stats,resid) importFrom(stats,pcauchy) importFrom(stats,model.matrix) importFrom(stats,var) -importFrom(stats,median) +importFrom(stats,median,quantile) importFrom(utils,globalVariables) importFrom(utils,installed.packages) importFrom(utils,packageVersion) importFrom(utils,read.table) importFrom(utils,setTxtProgressBar) importFrom(utils,txtProgressBar) -importFrom("methods", "as", "new") +importFrom("methods", "as", "new", "is") diff --git a/docs/pages/02_SPARK_Example.md b/docs/pages/02_SPARK_Example.md index f48e7e0..e0dd8b7 100644 --- a/docs/pages/02_SPARK_Example.md +++ b/docs/pages/02_SPARK_Example.md @@ -6,11 +6,12 @@ permalink: /02_SPARK_Example/ ### Example Analysis with SPARK: Breast Cancer Data -Load the `SPARK` package and Breast cancer data set, which can be downloaded [here](https://github.com/xzhoulab/SPARK/blob/master/data/Layer2_BC_Count.rds). +Load the `SPARK` package and Breast cancer dataset (included with the package; +can be also downloaded [here](https://github.com/xzhoulab/SPARK/blob/master/inst/extdata/Layer2_BC_Count.rds)). + ```R library('SPARK') - load("./Layer2_BC_Count.rds") - + load(system.file("extdata", "Layer2_BC_Count.rds", package = "SPARK")) ``` View the expression count matrix `rawcount`, each row denotes a gene and each column represents a cell/spot. ```R diff --git a/data/Layer2_BC_Count.rds b/inst/extdata/Layer2_BC_Count.rds similarity index 100% rename from data/Layer2_BC_Count.rds rename to inst/extdata/Layer2_BC_Count.rds