Browse code

removed test_Imports.R, pkg passes CHECK

paul-shannon authored on 23/01/2018 18:14:17
Showing4 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.19.20
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+Version: 1.19.22
5 5
 Date: 2018-01-23
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 Author: Paul Shannon, Matt Richards
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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@@ -7,7 +7,7 @@ strands: + -
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 Background letter frequencies
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 A 0.250 C 0.250 G 0.250 T 0.250 
9 9
 
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-MOTIF Mmusculus-cispb_1.02-M0082_1.02
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+MOTIF Mmusculus-cisbp_1.02-M0082_1.02
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 letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020
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  0.2203768432  0.3354050831  0.1020373584  0.3421807153
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  0.1117838556  0.1937497051  0.6695240896  0.0249423496
... ...
@@ -20,7 +20,7 @@ letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020
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  0.0551007724  0.0004313497  0.9430919013  0.0013759766
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  0.0952369898  0.3494527694  0.4354449644  0.1198652764
22 22
 
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-MOTIF Mmusculus-cispb_1.02-M0083_1.02
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+MOTIF Mmusculus-cisbp_1.02-M0083_1.02
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 letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020
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  0.1631992133  0.1296672588  0.1083071987  0.5988263292
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  0.2034461212  0.3491149401  0.2460171402  0.2014217985
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@@ -33,7 +33,7 @@ letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020
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  0.1006336198  0.0000926882  0.8991828391  0.0000908529
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  0.0001197413  0.0000375373  0.9998233202  0.0000194012
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-MOTIF Mmusculus-cispb_1.02-M0084_1.02
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+MOTIF Mmusculus-cisbp_1.02-M0084_1.02
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 letter-probability matrix: alength= 4 w= 10 nsites= 45 E=8.1e-020
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  0.1947249309  0.4000493650  0.1501429668  0.2550827372
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  0.0896002212  0.3254984788  0.5260297596  0.0588715404
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deleted file mode 100644
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@@ -1,221 +0,0 @@
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-library (MotifDb)
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-library (RUnit)
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-library (MotIV)
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-library (seqLogo)
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-#----------------------------------------------------------------------------------------------------
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-printf <- function(...) print(noquote(sprintf(...)))
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-#----------------------------------------------------------------------------------------------------
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-# Note: all matrix numbers were chosen randomly using "sample()"
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-runTests = function ()
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-{
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-
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-} # runTests
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-#----------------------------------------------------------------------------------------------------
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-test_cisbp <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/cisbp_matrix.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_cisbp
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-#----------------------------------------------------------------------------------------------------
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-test_FlyFactorSurvey <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/FlyFactorSurvey.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_FlyFactorSurvey
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-#----------------------------------------------------------------------------------------------------
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-test_HOCOMOCOv10 <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/HOCOMOCOv10.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_HOCOMOCOv10
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-#----------------------------------------------------------------------------------------------------
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-test_HOMER <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/HOMER.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_HOMER
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-#----------------------------------------------------------------------------------------------------
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-test_hPDI <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/hPDI.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_hPDI
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-#----------------------------------------------------------------------------------------------------
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-test_JASPAR_2014 <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/JASPAR_2014.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_JASPAR_2014
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-#----------------------------------------------------------------------------------------------------
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-test_JASPAR_CORE<- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/JASPAR_CORE.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_JASPAR_CORE
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-#----------------------------------------------------------------------------------------------------
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-test_jaspar2016 <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/jaspar2016.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_jaspar2016
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-#----------------------------------------------------------------------------------------------------
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-test_jolma2013 <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/jolma2013.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_jolma2013
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-#----------------------------------------------------------------------------------------------------
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-test_ScerTF <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/ScerTF.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_ScerTF
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-#----------------------------------------------------------------------------------------------------
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-test_stamlab <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/stamlab.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_stamlab
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-#----------------------------------------------------------------------------------------------------
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-test_SwissRegulon <- function(){
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-
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-    # Load the cisbp matrix as "cisbp"
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-    load("./single_matrices/SR_matrix.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "M0308_1.02"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(cisbp == queried))
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-    
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-} # test_SwissRegulon
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-#----------------------------------------------------------------------------------------------------
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-test_UniPROBE <- function(){
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-
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-    # Load the uniprobe matrix as "uniprobe"
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-    load("./single_matrices/UniPROBE_matrix.Rdata")
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-    
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-    # Matrix name
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-    mtx.name <- "UP00230"
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-
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-    # Query for the same matrix
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-    queried <- query(MotifDb, mtx.name)[[1]]
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-
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-    # Check that they're the same
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-    checkTrue(all(uniprobe == queried))
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-    
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-} # test_UniPROBE
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-
... ...
@@ -42,9 +42,10 @@ runTests = function ()
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   test.export_jasparFormatToFile()
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   test.geneToMotif()
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+  test.geneToMotif.ignore.jasparSuffixes()
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   test.motifToGene()
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-  test.associateTranscriptionFactors()
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+  test.associateTranscriptionFactors()
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 } # runTests
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 #------------------------------------------------------------------------------------------------------------------------
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 test.emptyCtor = function ()
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@@ -288,10 +289,10 @@ test.flyBindingDomains = function ()
288 289
 
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     # these counts will likely change with a fresh load of data from FlyFactorSurvey.
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-  checkEquals (tmp$Homeobox, 212)
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-  checkEquals (tmp[['zf-C2H2']], 160)
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-  checkEquals (tmp[["Helix-Turn-Helix"]], 182)
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-  checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 301) # lots of cisbp
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+  checkEquals(tmp$Homeobox, 212)
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+  checkEquals(tmp[['zf-C2H2']], 160)
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+  checkEquals(tmp[["Helix-Turn-Helix"]], 182)
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+  checkTrue(length(which(is.na(subset(x, organism=='Dmelanogaster')$bindingDomain))) > 300) # lots of cisbp
295 296
 
296 297
 } # test.flyBindingDomains
297 298
 #------------------------------------------------------------------------------------------------------------------------
... ...
@@ -563,7 +564,7 @@ test.export_memeFormatToFileDuplication = function ()
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   print ('--- test.export_memeFormatToFileDuplication')
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   mdb = MotifDb # ()
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   mdb.mouse = subset (mdb, organism=='Mmusculus')
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-  checkEquals (length (mdb.mouse), 1251)
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+  checkTrue(length(mdb.mouse) > 1300)
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   output.file = 'mouse.txt' # tempfile ()
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   max = 3
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   meme.text = export (mdb.mouse [1:max], output.file, 'meme')
... ...
@@ -771,7 +772,7 @@ test.geneToMotif <- function()
771 772
 
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       # MotifDb mode uses the MotifDb metadata, pulled from many sources
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    tbl.mdb <- geneToMotif(mdb, genes, source="mOtifdb")     # intentional mis-capitalization
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-   checkEquals(dim(tbl.mdb), c(12, 6))
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+   checkEquals(dim(tbl.mdb), c(13, 6))
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    checkEquals(subset(tbl.mdb, dataSource=="jaspar2016" & geneSymbol== "FOS")$motif, "MA0476.1")
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       # no recognizable (i.e., jaspar standard) motif name returned by MotifDb metadata
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       # MotifDb for ATF5
... ...
@@ -809,9 +810,11 @@ test.geneToMotif.ignore.jasparSuffixes <- function()
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       # this establishes the need for careful scrutiny as one winnows a geneToMotif result into
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       # useful non-reduplicative sequence analysis
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-   checkEquals(as.list(query(mdb, "MA0110599")), as.list(query(query(mdb, "MA0476.1"), "jaspar2018")))
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+   pfm.ma0110599 <- as.list(query(mdb, "MA0110599"))[[1]]
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+   pfm.ma0476.1  <- as.list(query(query(mdb, "MA0476.1"), "jaspar2018"))[[1]]
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+   checkEquals(pfm.ma0110599, pfm.ma0476.1)
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-} # test.geneToMotif
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+} # test.geneToMotif.ignore.jasparSuffixes
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 #------------------------------------------------------------------------------------------------------------------------
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 test.motifToGene <- function()
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 {
... ...
@@ -822,14 +825,15 @@ test.motifToGene <- function()
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       # MotifDb mode uses the MotifDb metadata "providerId",
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    tbl.mdb <- motifToGene(MotifDb, motifs, source="MotifDb")
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-   checkEquals(dim(tbl.mdb), c(3, 6))
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-   expected <- sort(c("MA0592.2", "ELF1.SwissRegulon", "UP00022"))
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+   checkEquals(dim(tbl.mdb), c(4, 6))
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+   expected <- sort(c("MA0592.2", "MA0592.2", "ELF1.SwissRegulon", "UP00022"))
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    actual <- sort(tbl.mdb$motif)
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    checkEquals(actual, expected)
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-   checkEquals(sort(tbl.mdb$geneSymbol), sort(c("Esrra", "ELF1", "Zfp740")))
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-   checkEquals(sort(tbl.mdb$dataSource), sort(c("jaspar2016", "SwissRegulon", "UniPROBE")))
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-   checkEquals(sort(tbl.mdb$organism),   sort(c("Mmusculus", "Hsapiens", "Mmusculus")))
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-   checkEquals(sort(tbl.mdb$source),     rep("MotifDb", 3))
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+   checkEquals(sort(tbl.mdb$geneSymbol), sort(c("ELF1", "Esrra", "Esrra", "Zfp740")))
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+   checkEquals(sort(tbl.mdb$dataSource), sort(c("jaspar2016", "jaspar2018", "SwissRegulon", "UniPROBE")))
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+
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+   checkEquals(sort(tbl.mdb$organism),   sort(c("Hsapiens", "Mmusculus", "Mmusculus", "Mmusculus")))
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+   checkEquals(tbl.mdb$source,     rep("MotifDb", 4))
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       # TFClass mode uses  TF family classifcation
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    tbl.tfClass <- motifToGene(MotifDb, motifs, source="TFClass")