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jyyulab · Aug 7, 2019 · d37743c · d37743c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,7 @@ License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: true
 Depends: 
-    R (>= 3.4.0),
+    R (>= 3.6.0),
     Matrix (>= 1.2-17),
     SummarizedExperiment (>= 1.14.0),
     lme4 (>= 1.1-21),

diff --git a/NetBID2_0.1.2.pdf b/NetBID2_0.1.2.pdf
diff --git a/R/pipeline_functions.R b/R/pipeline_functions.R
diff --git a/docs/docs/driver_estimation/driver_estimation.md b/docs/docs/driver_estimation/driver_estimation.md
@@ -419,12 +419,12 @@ NetBID.saveRData(analysis.par=analysis.par,step='ms-tab')
 
 - `out2excel()` can save multiple master tables as excel sheets in one EXCEL file.
 - For one master table, it consists of three parts:
-  - The first six columns are `originalID_label`, `originalID`, `gene_label`, `geneSymbol`, `funcType` and `Size`.
-    - `originalID_label` is the original ID type with suffix "_TF" or "_SIG", which should match the the ID type in `analysis.par$merge.network`, 
-    - `originalID` is the original ID type used in network construction, which should match the ID type in `analysis.par$cal.eset`, `analysis.par$DE`.
+- For one master table, it consists of three parts:
+  - The first six columns are `gene_label`, `geneSymbol`, `originalID`, `originalID_label`, `funcType` and `Size`.
     - `gene_label` is the driver's gene symbol or transcript symbol, with suffix "_TF" or "_SIG" to show driver's type. 
     - `geneSymbol` is the driver's gene symbol or transcript symbol, without suffix.
-`analysis.par$merge.ac.eset`,`analysis.par$DA`.
+    - `originalID` is the original ID type used in network construction, which should match the ID type in `analysis.par$cal.eset`, `analysis.par$DE`.
+    - `originalID_label` is the original ID type with suffix "_TF" or "_SIG", which should match the the ID type in `analysis.par$merge.network`, `analysis.par$merge.ac.eset`,`analysis.par$DA`.
     - **`originalID_label`** is the only column to ensure unique ID for row record.
     - `funcType` is either "TF" or "SIG" to mark driver's type. 
     - `Size` is number of target genes for the driver. 

diff --git a/docs/index.md b/docs/index.md
@@ -144,6 +144,7 @@ The tutorial contains three main parts, they can be followed by order or used in
 ## About the project
 
 For the detailed description of NetBID algorithm, please check our lab page [View Yu Lab@St. Jude](https://stjuderesearch.org/site/lab/yu).
+Email: xinran.dong@stjude.org or xinran.dong@foxmail.com
 
 ### License
 

diff --git a/inst/db/MOUSE/MOUSE_transcript.RData b/inst/db/MOUSE/MOUSE_transcript.RData
diff --git a/inst/db/Mus_musculus_gs2gene.RData b/inst/db/Mus_musculus_gs2gene.RData
diff --git a/man/draw.targetNet.TWO.Rd b/man/draw.targetNet.TWO.Rd