change package name

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: MAEio
+Package: PersonalisIO 
 Title: Read Various Data Sources into MultiAssayExperiment objects 
 Version: 0.1.9000
 Authors@R: 

README.md

@@ -1,4 +1,4 @@
-# Personalis-io
+# PersonalisIO
 
 **This package provides convenience functions for reading real-world evidence data provided by [Personalis](https://www.personalis.com/)
 into Bioconductor [MultiAssayExperiment](https://bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html) objects**

tests/testthat.R

@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/reference/test_package.html#special-files
 
 library(testthat)
-library(MAEio)
+library(PersonalisIO)
 
-test_check("MAEio")
+test_check("PersonalisIO")

vignettes/personalis.Rmd

@@ -14,20 +14,20 @@ knitr::opts_chunk$set(
 )
 ```
 
-This vignette demonstrates how to use the {Personalis-io} package to load Personalis 
+This vignette demonstrates how to use the {PersonalisIO} package to load Personalis 
 data into a {MultiAssayExperiment} object. 
 
 ```{r setup}
 suppressPackageStartupMessages({
-  library(MAEio)
+  library(PersonalisIO)
   library(purrr)
   library(conflicted)
   conflicts_prefer(base::setdiff)
 })
 ```
 
 Personalis ship their data in a (more or less) standardized directory structure 
-within one folder for each patient. The MAEio loader functions traverse this directory
+within one folder for each patient. The PersonalisIO loader functions traverse this directory
 structure and extract the different modalities. To load data from multiple patients 
 into a single object, we need a list of patient directories: 
 
@@ -45,10 +45,10 @@ We can now read a single modality into a {SummarizedExperiment}. For instance, t
 only.
 
 ```{r}
-personalis_gex <- MAEio::read_personalis_gene_expression(sample_list)
+personalis_gex <- PersonalisIO::read_personalis_gene_expression(sample_list)
 ```
 
-By inspecting the object, we can see, this imported gene expression data from 20 patients and ~23k genes. 
+By inspecting the object, we can see, this imported gene expression data from 5 patients and ~23k genes. 
 There are three different assays: `counts`, `tpm` and `normCounts`: 
 
 ```{r}
@@ -75,7 +75,7 @@ It is your repsonsibility to check the warnings carefully to make sure that
 all data that you expect to be there is successfully imported. 
 
 ```{r}
-mae <- MAEio::read_personalis(sample_list)
+mae <- PersonalisIO::read_personalis(sample_list)
 ```
 
 Here's an overview of the {MultiAssayExperiment} object with all available