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removed non-essential packages

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reubenthomas 2020-11-11 15:19:07 -08:00
parent 8cc733f674
commit ccb1d59013
1 changed files with 47 additions and 8 deletions
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single-cell-analysis/Session_3/Session3.html
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@ -396,12 +396,9 @@ rm(list = ls())
suppressMessages(library(Seurat))
suppressMessages(library(muscat))
suppressMessages(library(SummarizedExperiment))
suppressMessages(library(dplyr))
suppressMessages(library(tidyverse))
suppressMessages(library(magrittr))
suppressMessages(library(purrr))
suppressMessages(library(tibble))
suppressMessages(library(gdata))
suppressMessages(library(tidyr))
#source a function I slightly modified from the muscat package for the within-cluster multi-sample multi-condition comparison
source("pbDS_update.R")
@ -631,7 +628,7 @@ print(sprintf("After filtering outliers: %d cells and %d genes", ncol(
|
|======================================================================| 100%</code></pre>
<pre><code>## Calculating gene attributes</code></pre>
<pre><code>## Wall clock passed: Time difference of 2.525825 secs</code></pre>
<pre><code>## Wall clock passed: Time difference of 2.565716 secs</code></pre>
<pre><code>## Determine variable features</code></pre>
<pre><code>## Set 3000 variable features</code></pre>
<pre><code>## Place corrected count matrix in counts slot</code></pre>
@ -897,6 +894,48 @@ ClusterRes &lt;- sapply(Clusters, estimateCellStateChange, Ncells, TotalCells, S
<pre><code>## The following object is masked from 'package:S4Vectors':
##
## expand</code></pre>
<pre><code>## Loading required package: gdata</code></pre>
<pre><code>## gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.</code></pre>
<pre><code>## </code></pre>
<pre><code>## gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.</code></pre>
<pre><code>##
## Attaching package: 'gdata'</code></pre>
<pre><code>## The following objects are masked from 'package:dplyr':
##
## combine, first, last</code></pre>
<pre><code>## The following object is masked from 'package:purrr':
##
## keep</code></pre>
<pre><code>## The following object is masked from 'package:SummarizedExperiment':
##
## trim</code></pre>
<pre><code>## The following object is masked from 'package:Biobase':
##
## combine</code></pre>
<pre><code>## The following object is masked from 'package:GenomicRanges':
##
## trim</code></pre>
<pre><code>## The following object is masked from 'package:IRanges':
##
## trim</code></pre>
<pre><code>## The following objects are masked from 'package:S4Vectors':
##
## first, first&lt;-</code></pre>
<pre><code>## The following object is masked from 'package:BiocGenerics':
##
## combine</code></pre>
<pre><code>## The following object is masked from 'package:stats4':
##
## nobs</code></pre>
<pre><code>## The following object is masked from 'package:stats':
##
## nobs</code></pre>
<pre><code>## The following object is masked from 'package:utils':
##
## object.size</code></pre>
<pre><code>## The following object is masked from 'package:base':
##
## startsWith</code></pre>
<pre><code>## [1] &quot;Cluster 0&quot;
## [1] &quot;Cluster 1&quot;
## [1] &quot;Cluster 3&quot;
@ -949,7 +988,7 @@ for (i in 1:length(batch.list)) {
<pre><code>## Second step: Get residuals using fitted parameters for 13831 genes</code></pre>
<pre><code>## Computing corrected count matrix for 13831 genes</code></pre>
<pre><code>## Calculating gene attributes</code></pre>
<pre><code>## Wall clock passed: Time difference of 2.014113 secs</code></pre>
<pre><code>## Wall clock passed: Time difference of 1.96617 secs</code></pre>
<pre><code>## Warning: The 'show_progress' argument is deprecated as of v0.3. Use 'verbosity'
## instead. (in sctransform::vst)</code></pre>
<pre><code>## Calculating cell attributes from input UMI matrix: log_umi</code></pre>
@ -962,7 +1001,7 @@ for (i in 1:length(batch.list)) {
<pre><code>## Second step: Get residuals using fitted parameters for 13981 genes</code></pre>
<pre><code>## Computing corrected count matrix for 13981 genes</code></pre>
<pre><code>## Calculating gene attributes</code></pre>
<pre><code>## Wall clock passed: Time difference of 1.47981 secs</code></pre>
<pre><code>## Wall clock passed: Time difference of 1.38957 secs</code></pre>
<pre class="r"><code>## Select features to identify anchors
batch.features &lt;- SelectIntegrationFeatures(object.list = batch.list, nfeatures = 3000)
batch.list &lt;- PrepSCTIntegration(object.list = batch.list, anchor.features = batch.features,