readme

README.md

@@ -1 +1,48 @@
-# cancerCellNet
+# cancerCellNet (cCN)
+
+
+#### Setup
+```R
+library(devtools)
+install_github("pcahan1/cancerCellNet", ref="master", auth="your_token_here")
+library(cancerCellNet)
+
+```
+
+#### Load cnProc and query data
+```R
+mydate<-utils_myDate()
+cnProc<-utils_loadObject("cnProc_cancer_Mar_23_2018.rda")
+v.genes<-rownames(cnProc$expTrain)
+length(v.genes)
+[1] 19398
+
+expQList<-utils_loadObject("expGeneList_lgg-CCLE.R")
+stQuery<-utils_loadObject("sampTab_lgg-CCLE_QC.R")
+```
+
+#### Transform query data
+```R
+expQuery<-expQList[['counts']][v.genes,]
+expQueryNorm<-trans_rnaseq(expQuery, 1e5)
+```
+
+#### Analyze query data and plot
+```R
+lgg_res<-cn_apply(expQueryNorm, stQuery, cnProc)
+cn_HmClass(lgg_res, isBig=F)
+fname<-paste0("hmClass_lgg_", mydate, ".png")
+dev.copy(png, file=fname, units='in',width=8, height=4, res=300)
+dev.off()
+```
+![](md_img/hmClass_lgg_Mar_26_2018.png)
+
+
+####cnProc files:
+
+| DATE | cnProc | 
+|------|--------|
+| Mar_23_2018 | [Download](https://s3.amazonaws.com/cellnet-rnaseq/ref/cnproc/HS/cnProc_cancer_Mar_23_2018.rda) |
+
+
+