Update vignette and bioc-check yml file.

.github/workflows/check-bioc.yaml

@@ -54,12 +54,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
           # - { os: ubuntu-latest, r: '4.3.3', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          # - { os: ubuntu-latest, r: 'devel', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
           # - { os: ubuntu-latest, r: '4.3.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.3.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3.3', bioc: '3.18'}
+          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          - { os: windows-latest, r: '4.4', bioc: '3.19'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
 
@@ -70,7 +70,7 @@ jobs:
       TZ: UTC
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      UPGRADE_PKGS: ${{ matrix.config.bioc >= '3.18' }}
+      UPGRADE_PKGS: ${{ matrix.config.bioc >= '3.19' }}
 
     steps:
       ## Set the R library to the directory matching the

vignettes/smartid_Demo.Rmd

@@ -32,7 +32,7 @@ knitr::opts_chunk$set(
 
 **smartid**
 
-`smartid` is a package that enables automated selection of group specific signature, especially for rare population. This package is developed for generating specifc lists of signature genes based on TF-IDF modified methods for labeled data. It can also be used as a new gene-set scoring method or data transformation method for un-labeled data. Multiple visualization functions are implemented in this package.
+`smartid` is a package that enables automated selection of group specific signature genes, especially for rare population. This package is developed for generating lists of specific signature genes based on **Term Frequency-Inverse Document Frequency** (TF-IDF)  modified methods and **expectation maximization** (EM) for labeled data. It can also be used as a new gene-set scoring method or data transformation method for un-labeled data. Multiple visualization functions are implemented in this package.
 
 # Installation
 
@@ -105,7 +105,12 @@ data_sim
 
 ## Score Samples
 
-The first step is to score all samples/cells by using specified approach. The score can be composed of 3 terms: TF (term/feature frequency), IDF (inverse document/cell frequency) and IAE (inverse average expression of features). Each term has a couple of available choices with different formats to suit labeled or un-labeled data.
+The first step is to score all samples/cells by using specified approach. The score can be composed of 3 terms: TF (term/feature frequency), IDF (inverse document/cell frequency) and IAE (inverse average expression of features). Each term has a couple of available choices with different formats to suit labeled or un-labeled data. Users can use function `idf_iae_methods()` to see available methods for IDF/IAE term. More details of each term can be seen in help page of each function, e.g. `?smartid:::idf`.
+
+```{r}
+## show available methods
+idf_iae_methods()
+```
 
 The basic version of TF, IDF and IAE can be termed as:
 $$\mathbf{TF_{i,j}}=\frac{N_{i,j}}{\sum_j{N_{i,j}}}$$