update R package

README.md

@@ -87,8 +87,7 @@ ggplot(dat, aes(x=score,color=name))+ theme_bw()  + geom_density(size=1.5)+scale
 ggsave(“ScoreDistribution.png”, plot = last_plot(), device = “png”)
 ```
 
-When you decide for the threshold you can visualize the resulted network (see section [Visualization of the network](### Visualization of the network
-) ) and get all the links with a score higher than the threshold (see subsection [Get only the links with a score higher than a threshold](####Get only the links with a score higher than a threshold) )
+When you decide for the threshold you can visualize the resulted network (see section [Visualization of the network](#visualization-of-the-network) ) and get all the links with a score higher than the threshold (see subsection [Get only the links with a score higher than a threshold](#get-only-the-links-with-a-score-higher-than-a-threshold) )
 
 
 However, we provide a threshold selection method based on the [fisher z-transformation](https://en.wikipedia.org/wiki/Fisher_transformation). You can compute the threshold for the DREAM4 data with the following command where:
@@ -99,18 +98,18 @@ However, we provide a threshold selection method based on the [fisher z-transfor
 * `nvar` is the number of variables (number of columns of input matrix for (reg-)DPM )
 
 ```r
-fisher_test(dpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$threshold
-fisher_test(regdpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$threshold
+tr <- fisher_test(dpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$threshold
+tr <- fisher_test(regdpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$threshold
 ```
 
 You can also get all the significant links based on fisher z-transformation at significance level alpha:
 ```r
-fisher_test(dpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$Listlink
-fisher_test(regdpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$Listlink
+dpm_sig_links <- fisher_test(dpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$Listlink
+regdpm_sig_links <- fisher_test(regdpmres, alpha=0.05, nsamp=nrow(dream4), nnodes=ncol(dream4))$Listlink
 ```
 
 As an alternative, you can select the top-ranked links based on (reg.)DPM score which are most likely to be true links.
-See section [Get only the top-ranked links](####get only the top-ranked links)
+See section [Get only the top ranked links](#get-only-the-top-ranked-links)
 
 ### Get the list of the links
 You need to first install the necessary R packages from CRAN:
@@ -146,7 +145,7 @@ regdpm_links <- get_link(regdpmres,threshold = 0.2)
 dim(regdpm_links)
 head(regdpm_links)
 ```
-#### Get only the top-ranked links
+#### Get only the top ranked links
 
 If you are interested in extracting the top links with the highest scores, use the parameter `top_ranked` and specify the number of top-ranked links to report: