Update

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: miRSM
 Type: Package
 Title: Inferring miRNA sponge modules in heterogeneous data
-Version: 1.99.3
+Version: 1.99.4
 Authors@R: 
     person(given = "Junpeng", 
            family = "Zhang", 

NEWS

@@ -1,4 +1,4 @@
-CHANGES IN VERSION 1.99.0-1.99.3
+CHANGES IN VERSION 1.99.0-1.99.4
 -------------------------
 o Add new methods for identifying miRNA sponge modules <2024-02-04, Sun>
 

README.md

@@ -1,7 +1,7 @@
 # miRSM R package
 
 # Introduction
-This package provides several utility functions to infer miRNA sponge or ceRNA modules at single-sample and multi-sample levels.
+This package provides several utility functions to study miRNA sponge or ceRNA modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.
 
 # Installation
 ```{r echo=FALSE, results='hide', message=FALSE}
@@ -18,16 +18,16 @@ suppressMessages(library(miRSM))
 # Load BRCA sample data
 data(BRCASampleData)
 
-# Identify ceRNA-mRNA co-expression modules using WGCNA
+# Identifying gene co-expression modules using WGCNA
 modulegenes_WGCNA <- module_WGCNA(ceRExp[, seq_len(150)], 
                                   mRExp[, seq_len(150)])
 
-# Identify miRNA sponge modules using sensitivity RV coefficient (SRVC)
+# Identifying miRNA sponge modules using sensitivity RV coefficient (SRVC)
 miRSM_WGCNA_SRVC <- miRSM(miRExp, ceRExp, mRExp, miRTarget, 
                         modulegenes_WGCNA, method = "SRVC",
                         SMC.cutoff = 0.01, RV_method = "RV")
                         
-# Identify sample-specific miRNA sponge modules
+# Identifying sample-specific miRNA sponge modules
 nsamples <- 3
 modulegenes_igraph_all <- module_igraph(ceRExp[, 151:300], mRExp[, 151:300])
 modulegenes_WGCNA_exceptk <- lapply(seq(nsamples), function(i) module_WGCNA(ceRExp[-i, seq(150)], mRExp[-i, seq(150)]))
@@ -59,14 +59,14 @@ miRSM.Validate <- module_Validate(miRSM_WGCNA_SRVC_genes, Groundtruth)
 # Co-expression analysis of miRNA sponge modules
 miRSM_WGCNA_Coexpress <-  module_Coexpress(ceRExp, mRExp, miRSM_WGCNA_SRVC_genes, resample = 10, method = "mean", test.method = "t.test")
 
-# miRNA distribution analysis of sharing miRNAs
+# Distribution analysis of sharing miRNAs
 miRSM_WGCNA_share_miRs <-  share_miRs(miRTarget, miRSM_WGCNA_SRVC_genes)
 miRSM_WGCNA_miRdistribute <- module_miRdistribute(miRSM_WGCNA_share_miRs)
 
-# Predict miRNA-target interactions
+# Predicting miRNA-target interactions
 miRSM_WGCNA_miRtarget <- module_miRtarget(miRSM_WGCNA_share_miRs, miRSM_WGCNA_SRVC_genes)
 
-# Identify miRNA sponge interactions
+# Identifying miRNA sponge interactions
 miRSM_WGCNA_miRsponge <- module_miRsponge(miRSM_WGCNA_SRVC_genes)
 
 ```