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krishan57gupta · Apr 18, 2020 · 8a7eaaf · 8a7eaaf
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diff --git a/R/iCTC.R b/R/iCTC.R
@@ -337,7 +337,7 @@ NB <- function(data_case,te)
                      'nb',trControl=caret::trainControl(method='cv',
                     number=5, returnResamp = "all"))
     test_prediction_1 <-stats::predict(fit,te)
-    test_prob <-stats::predict(iCTC::fit,te,type="prob")
+    test_prob <-stats::predict(fit,te,type="prob")
     }
     return_list <- list("te_labels"=as.numeric(as.matrix(test_prediction_1)),
                       "te_probCTC"=as.numeric(test_prob[,1]),

diff --git a/README.Rmd b/README.Rmd
@@ -51,7 +51,7 @@ library(iCTC)
 ```
 
 ```{r data, message=FALSE,warning = FALSE,include=TRUE, cache=FALSE}
-cell_samples=iCTC::raw_test_data$Clearcell_Polaris_sample_test
+cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
 head(cell_samples)
 ```
 

diff --git a/README.md b/README.md
@@ -40,7 +40,7 @@ library(iCTC)
 ```
 
 ``` r
-cell_samples=iCTC::raw_test_data$Clearcell_Polaris_sample_test
+cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
 head(cell_samples)
 #>          Ctc_Naveen_1850-061-049-CS26_S19_15
 #> CDH2                                    0.00

diff --git a/doc/iCTC.R b/doc/iCTC.R
@@ -8,7 +8,7 @@ knitr::opts_chunk$set(
 library(iCTC)
 
 ## ----data, message=FALSE,warning = FALSE,include=TRUE, cache=FALSE------------
-cell_samples=iCTC::raw_test_data$Clearcell_Polaris_sample_test
+cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
 head(cell_samples)
 
 ## ----main, message=FALSE,warning = FALSE, include=TRUE, cache=FALSE-----------

diff --git a/doc/iCTC.Rmd b/doc/iCTC.Rmd
@@ -51,7 +51,7 @@ Libraries need to be loaded before running iCTC.
 library(iCTC)
 ```
 ```{r data, message=FALSE,warning = FALSE,include=TRUE, cache=FALSE}
-cell_samples=iCTC::raw_test_data$Clearcell_Polaris_sample_test
+cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
 head(cell_samples)
 ```
 

diff --git a/doc/iCTC.html b/doc/iCTC.html
@@ -323,7 +323,7 @@ <h2>Vignette tutorial</h2>
 <p>This vignette uses a small dataset of cell samples, which is saved in package itself, to demonstrate a standard pipeline. This vignette can be used as a tutorial as well.</p>
 <p>Libraries need to be loaded before running iCTC.</p>
 <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(iCTC)</a></code></pre></div>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">cell_samples=iCTC<span class="op">::</span>raw_test_data<span class="op">$</span>Clearcell_Polaris_sample_test</a>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">cell_samples&lt;-iCTC<span class="op">::</span>raw_test_data<span class="op">$</span>Clearcell_Polaris_sample_test</a>
 <a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw">head</span>(cell_samples)</a>
 <a class="sourceLine" id="cb4-3" data-line-number="3"><span class="co">#&gt;          Ctc_Naveen_1850-061-049-CS26_S19_15</span></a>
 <a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#&gt; CDH2                                    0.00</span></a>

diff --git a/vignettes/iCTC.Rmd b/vignettes/iCTC.Rmd
@@ -51,7 +51,7 @@ Libraries need to be loaded before running iCTC.
 library(iCTC)
 ```
 ```{r data, message=FALSE,warning = FALSE,include=TRUE, cache=FALSE}
-cell_samples=iCTC::raw_test_data$Clearcell_Polaris_sample_test
+cell_samples<-iCTC::raw_test_data$Clearcell_Polaris_sample_test
 head(cell_samples)
 ```