From 617637b7933328689212d2de5f463d7f6873f461 Mon Sep 17 00:00:00 2001 From: FelixErnst Date: Mon, 7 Dec 2020 08:09:42 +0100 Subject: [PATCH] typo fixes --- .github/workflows/build-book-release.yml | 4 ++-- 13-microbiome-exploration.Rmd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-book-release.yml b/.github/workflows/build-book-release.yml index 80062073d..b4c6e81c5 100644 --- a/.github/workflows/build-book-release.yml +++ b/.github/workflows/build-book-release.yml @@ -88,8 +88,8 @@ jobs: uses: actions/cache@v1 with: path: ${{ env.R_LIBS_USER }} - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-pkgUpdate1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-pkgUpdate1- - name: Install BiocManager run: | diff --git a/13-microbiome-exploration.Rmd b/13-microbiome-exploration.Rmd index 21bad1ce0..2f3d2eed1 100644 --- a/13-microbiome-exploration.Rmd +++ b/13-microbiome-exploration.Rmd @@ -77,8 +77,8 @@ head(getPrevalence(se, rank = "Phylum", detection = 1/100, sort = TRUE, abund_values = "counts", as_relative = TRUE)) ``` -The differnence in the naming scheme, is that by default `na.rm = TRUE` is used -for agglomoration in `getPrevalence`, whereas the default for +The difference in the naming scheme, is that by default `na.rm = TRUE` is used +for agglomeration in `getPrevalence`, whereas the default for `agglomerateByRank` is `FALSE` to prevent accidental data loss. If you only need the names of the prevalent taxa, `getPrevalentTaxa` is