version 1.0

cran · Oct 3, 2015 · 071ebd0 · 071ebd0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,13 @@
 Package: MetaPath
 Type: Package
-Title: Perform the Meta-Analysis for Pathway Enrichment analysis
-        (MAPE).
-Version: 0.9
-Date: 2011-05-20
+Title: Perform the Meta-Analysis for Pathway Enrichment Analysis (MAPE)
+Version: 1.0
+Date: 2015-09-28
 Author: Kui Shen and Geroge Tseng
 Maintainer: Kui Shen <kuishen@alumni.pitt.edu>
-Depends: R(>=
-        2.13.0),Biobase,AnnotationDbi,genefilter,GSEABase,limma,impute,qvalue
-Description: This R package was implemented to perform the
-        Meta-analysis for Pathway Enrichment (MAPE) methods introduced
-        by Shen and Tseng (2010). It includes functions to
+Depends: R (>= 3.0.0),Biobase,GSEABase,genefilter,impute
+Description: Perform the Meta-analysis for Pathway Enrichment (MAPE) 
+		methods introduced by Shen and Tseng (2010). It includes functions to
         automatically perform MAPE_G (integrating multiple studies at
         gene level), MAPE_P (integrating multiple studies at pathway
         level) and MAPE_I (a hybrid method integrating MAEP_G and
@@ -28,6 +25,7 @@ Description: This R package was implemented to perform the
         http://www.ncbi.nlm.nih.gov/pubmed/20410053.
 License: GPL (>= 2.0)
 LazyLoad: yes
-Packaged: 2012-05-22 19:18:14 UTC; kshen
+NeedsCompilation: no
+Packaged: 2015-10-02 19:12:17 UTC; root
 Repository: CRAN
-Date/Publication: 2012-05-23 07:37:18
+Date/Publication: 2015-10-03 07:57:54
diff --git a/MD5 b/MD5
@@ -1,33 +1,31 @@
-c9c591ec4e597cd8c4044b462ba194b4 *DESCRIPTION
-9b873795e5bb10af240a21e31b15fc47 *NAMESPACE
-4317920ec32f15f9dc6eaf3e6746932e *R/Affy2GeneID.R
-658aba7085d560f0fc4d7c8e0b25eca7 *R/Enrichment_KS_gene.R
+af53aab3956ea245dd990cf477dfcb34 *DESCRIPTION
+ccdc1a9d1493c2d2e9a606df80ee02a5 *NAMESPACE
+5f7166931ddb801c964f7a31883f96ff *R/Enrichment_KS_gene.R
 54509027b120bff4c6b20c64497d3e7a *R/Enrichment_KS_sample.R
-1c39dedba9906b7ab94c1714fe1d4d7e *R/F.perm.sample.R
-ea5f874db3fe6f25400a490b85dfb618 *R/MAPE.R
+282bc5b894ee45f84e73d2f0f89a026b *R/F.perm.sample.R
+c05526ecb693c51fc69a37be915f10d8 *R/MAPE.R
 7335fecee0bfc3651987f50644ac24ed *R/MAPE_G_gene_KS.R
 05a24098c4803a901b1b5ac4e82e2c07 *R/MAPE_G_sample_KS.R
 10445ab6711ade2f26b5d7d9fe7afdb5 *R/MAPE_I_KS.R
 41aa5e7e7cc65afaede3caf65f4f9f95 *R/MAPE_P_gene_KS.R
 637a0e5acddc6b31ed04795ec024ab1c *R/MAPE_P_sample_KS.R
-ff493dbfdfe2b8af1269119b038e2d2b *R/Tperm.sample.R
-70c7e306f3e75278ac51940a5c5a4ce5 *R/cor.func.R
-8d52ff267b5dec812af8b1a6d12b2451 *R/cox.perm.sample.R
-97162bec4385f352eca63907c1c8d9d1 *R/coxfunc.R
-6515c7362b56f2dae5903130ae6b7ff3 *R/coxscor.R
-0e610edc68697f60cf15f5e3ab39a921 *R/coxstuff.R
-e5c87c8f3e2f0ea455684071d34df8d0 *R/coxvar.R
-fc90ad6fa5876632f32bab7ead419d04 *R/plotMAPE.R
+78c7f82c8f81bb33b50413b6dd635bef *R/Tperm.sample.R
+453bbe483865717685fb666fe17e35db *R/cor.func.R
+7db52c0ad3dce8f22ade25aadb5cbc69 *R/cox.perm.sample.R
+7a18ed5fd3283a266035ab5a97fcd9fb *R/coxfunc.R
+a1d97b05d054eb9fc7040c2ae67d0005 *R/coxscor.R
+f4dd0963718574cfc09ffab8804e0833 *R/coxstuff.R
+426867e5b25164e122976e800d15f513 *R/coxvar.R
+74229d20b0e72c5e3daba23db49bd832 *R/plotMAPE.R
 d655dbc34809ba016e25e6743f276784 *R/pqvalues.compute.R
 e6ec1a0101a80f066b885e571b2ed7ea *R/reg.perm.sample.R
 ce49c5b4ce45f8730e0502e3fefd936e *data/MAQC.rda
 e98c7cabd751d9c5c4da6d3195a1d53c *data/datalist
 562cf4a6471842c0558b121e3238bb6b *data/pathway.DB.rda
-8e391ea31a2a4971dc333c77cfcf6ac0 *man/Affy2GeneID.Rd
 4eefc8c720642ecfd0afd44ef2471f13 *man/Enrichment_KS_gene.Rd
 1aa226e58b29b881506821d05234f4d1 *man/Enrichment_KS_sample.Rd
 f0825f195b30dc85a6a642df8d9e5b2f *man/F.perm.sample.Rd
-411d8f44a3eb1c07d23c4034f7f2dc37 *man/MAPE.Rd
+94afa62bfafc7c20f6d4ca6b5175aa9e *man/MAPE.Rd
 8813bb62851092b12afebf0e73e6e1d4 *man/MAPE_G_gene_KS.Rd
 aef491ae1c6219b637eaae39fb041c2a *man/MAPE_G_sample_KS.Rd
 e13d5624158f67a53111259e0034ee19 *man/MAPE_I_KS.Rd
@@ -36,13 +34,13 @@ e13d5624158f67a53111259e0034ee19 *man/MAPE_I_KS.Rd
 9a7acfd1219e6d4b3893c1cfb692af74 *man/MAQC.Rd
 30bf454c2efb54d9391c1a686268946a *man/MetaPath-package.Rd
 58d037cf696b94b721e05a86c6c89e3a *man/Tperm.sample.Rd
-25157f528153efecb501544382018c3e *man/cor.func.Rd
-e218986b56bfdbd282a7eb78ce5c9e86 *man/cox.perm.sample.Rd
-b18541789827e876f300181cbb037397 *man/coxfunc.Rd
-2a33f205892523cf65b3f3d8b94d7713 *man/coxscor.Rd
-9fdb6df91584067755829932afc8f527 *man/coxstuff.Rd
-5a521da68e2da67676c674b5eb6b1ee3 *man/coxvar.Rd
+b29943791f320c675de460283ac82d12 *man/cor.func.Rd
+f48d690bf1f1f3a8388844ae694995d7 *man/cox.perm.sample.Rd
+4c8b6dcac691e52f737cadc07f5a2c3e *man/coxfunc.Rd
+90f83acdfc73e58b39abe28552c7ff96 *man/coxscor.Rd
+bc042e74a1c3c719a4bd9c24214ebe21 *man/coxstuff.Rd
+938131adc635f4b9b7c2919a96da5f6c *man/coxvar.Rd
 7962389c4121a46b2b05aead7499e33a *man/pathway.DB.Rd
-886b3d71b8cf4407c73232da3b6f5e31 *man/plotMAPE.Rd
+e6cdebc23e35cfd8615671a23ade9997 *man/plotMAPE.Rd
 1636cd8cd20e14683c34a50b1b637c7f *man/pqvalues.compute.Rd
 b84742c506911e9e11547689cf59a2b6 *man/reg.perm.sample.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,4 @@
 export( 
-Affy2GeneID,
 cor.func,
 cox.perm.sample,
 coxfunc,
@@ -19,12 +18,14 @@ pqvalues.compute,
 reg.perm.sample,
 Tperm.sample
 )
+
 import(
 Biobase,
-AnnotationDbi,
-genefilter,
 GSEABase,
-limma,
-impute,
-qvalue
+genefilter,
+impute
 )
+
+importFrom("grDevices", "gray")
+importFrom("stats", "heatmap", "p.adjust", "pchisq")
+
diff --git a/R/Enrichment_KS_gene.R b/R/Enrichment_KS_gene.R
@@ -25,13 +25,13 @@ if(!is.null(madata)){
 
 
 	if(resp.type=="twoclass") {	
-		tstat=rowttests(exprs(madata), as.factor(label), tstatOnly= F)
+		tstat=genefilter::rowttests(exprs(madata), as.factor(label), tstatOnly= F)
 		p.values=(tstat$p.value)
 		names(p.values)=rownames(tstat)
 		gene.name.sort=names(sort(p.values, decreasing = F))
 
 	} else if(resp.type=="multiclass") {	
-		tstat=rowFtests(exprs(madata), as.factor(label), var.equal = TRUE)
+		tstat=genefilter::rowFtests(exprs(madata), as.factor(label), var.equal = TRUE)
 		p.values=(tstat$p.value)
 		names(p.values)=rownames(tstat)
 		gene.name.sort=names(sort(p.values, decreasing = F))

diff --git a/R/F.perm.sample.R b/R/F.perm.sample.R
@@ -1,11 +1,11 @@
 F.perm.sample <-
 function(x, fac, nperm) {
-    obs = rowFtests(x, fac, var.equal = TRUE)$statistic
+    obs = genefilter::rowFtests(x, fac, var.equal = TRUE)$statistic
 	names(obs)=rownames(x)
 	perms= matrix(NA,  nrow(x),  nperm)
 
 	for(t1 in 1:nperm){
-		perms[,t1]=rowFtests(x, sample(fac), var.equal = TRUE)$statistic
+		perms[,t1]=genefilter::rowFtests(x, sample(fac), var.equal = TRUE)$statistic
 	}
 	rownames(perms)=rownames(x)
 	colnames(perms)=paste('B',1:nperm,sep="")