When retention time is not provided, m/z vector can still be used to
check reaction level changes. You might use getrda to find
-the high frequncy PMDs.
data(spmeinvivo)
# get the m/z
@@ -886,7 +886,8 @@ Reactomics analysis for MS only da
#> [8] "14.015" "17.026" "18.011" "21.982" "28.031" "28.032" "44.026"
#> [15] "67.987" "67.988" "88.052" "116.192" "135.974" "135.975"
-hfpmd <- as.numeric(colnames(sda))# save them as numeric vector
+hfpmd <- as.numeric(colnames(sda))
Then getpmddf function can be used to extract all the
paired ions for certain PMD.
@@ -923,7 +924,7 @@Reactomics analysis for MS only da pmdinsstaticscale <- t(scale(t(pmdinsstatic))) # get the pmd static intensity across samples pmdinsstaticall <- apply(pmdinsstaticscale,2,sum) -# show the PMD static intensity +# show the PMD static intensity for each sample pmdinsstaticall #> 1405_Fish1_F1 1405_Fish1_F2 1405_Fish1_F3 1405_Fish2_F1 1405_Fish2_F2 #> 1.027100 -16.703628 2.373645 -27.241358 12.433566 @@ -944,7 +945,7 @@
Reactomics analysis for MS only da pmdinsdynamic[idx,] <- 1/ratio[rsdidx,][idx,] # get the pmd dynamic intensity across samples pmdinsdynamicall <- apply(pmdinsdynamic,2,sum) -# show the PMD dynamic intensity +# show the PMD dynamic intensity for each sample pmdinsdynamicall #> 1405_Fish1_F1 1405_Fish1_F2 1405_Fish1_F3 1405_Fish2_F1 1405_Fish2_F2 #> 374.1957 315.6090 388.0063 207.8236 233.4380 diff --git a/docs/index.html b/docs/index.html index 69a0379..f941e84 100644 --- a/docs/index.html +++ b/docs/index.html @@ -95,7 +95,7 @@
Installation
You can install package from this GitHub repository:
-+
{r} devtools::install_github("yufree/pmd")
{r} remotes::install_github("yufree/pmd")Or find a stable version from CRAN:
{r} install.packages('pmd')
For MS only data such as FT-ICR or MS imaging data, check the section of “Reactomics analysis for MS only data” in Reactomics Analysis Tutorial or this blog post.
PMD analysis paper. This paper proposed structure/reaction directed analysis with PMD.
Reactomics paper. This paper contained the concepts of PMD based reactomics, applications and data mining of reaction database and compounds database.
Slides. This is the slides for ASMS 2020 Reboot and here is the video of presentation. Press “P” and you will see the notes for each slide with details. Another full version of reactomics presentation for one hour presentation could be found here. I will not update the conference presentation while I will add new contents for the full version of reactomics presentation whenever I have new results.