1. TDbasedUFEadv
  2. man
  3. selectFeatureTransRect.Rd
Browse code

v-0.99.17

tagtag authored on 24/03/2023 16:44:34
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ 765e042
... ... 
@@ -10,7 +10,7 @@ selectFeatureTransRect(
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   cond,
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   de = rep(1e-04, 2),
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   p0 = 0.01,
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-  breaks = as.integer(100),
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+  breaks = 100L,
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   input_all = NULL
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 )
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 }
Browse code

v-0.99.16

tagtag authored on 22/03/2023 15:27:20
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ 5bd8090
... ... 
@@ -37,12 +37,12 @@ Select features for a tensor generated from two matrices that
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  share samples.
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 }
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 \examples{
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-require(TDbasedUFE)
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+library(TDbasedUFE)
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 set.seed(0)
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 matrix1 <- matrix(runif(1000),20) #row features, column samples
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 matrix2 <- matrix(runif(2000),40) #row features, column samples
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 Z <- prepareTensorfromMatrix(t(matrix1),t(matrix2))
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-Z <- prepareSummarizedExperimentTensorRect(sample=as.character(seq_len(50)),
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+Z <- prepareTensorRect(sample=as.character(seq_len(50)),
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 feature=list(as.character(seq_len(20)),as.character(seq_len(40))),
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 sampleData=list(rep(seq_len(2),each=25)),value=Z)
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 HOSVD <- computeHosvd(Z)
Browse code

v-0.99.14

tagtag authored on 21/03/2023 10:32:47
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ 5b757d8
... ... 
@@ -38,13 +38,15 @@ Select features for a tensor generated from two matrices that
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 }
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 \examples{
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 require(TDbasedUFE)
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-matrix1 <- matrix(runif(10000),200) #row features, column samples
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-matrix2 <- matrix(runif(20000),400) #row features, column samples
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+set.seed(0)
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+matrix1 <- matrix(runif(1000),20) #row features, column samples
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+matrix2 <- matrix(runif(2000),40) #row features, column samples
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 Z <- prepareTensorfromMatrix(t(matrix1),t(matrix2))
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 Z <- prepareSummarizedExperimentTensorRect(sample=as.character(seq_len(50)),
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-feature=list(as.character(seq_len(200)),as.character(seq_len(400))),
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+feature=list(as.character(seq_len(20)),as.character(seq_len(40))),
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 sampleData=list(rep(seq_len(2),each=25)),value=Z)
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 HOSVD <- computeHosvd(Z)
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 cond <- list(attr(Z,"sampleData")[[1]],NULL,NULL)
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-index_all <- selectFeatureTransRect(HOSVD,cond,de=c(0.01,0.01),input_all=2)
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+index_all <- selectFeatureTransRect(HOSVD,cond,de=c(0.1,0.1),
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+input_all=2,p0=1e-10)
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 }
Browse code

v-0.99.9

tagtag authored on 20/03/2023 13:52:28
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ c54d04c
... ... 
@@ -2,7 +2,7 @@
2 2 
 % Please edit documentation in R/selectFeatureTransRect.R
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 \name{selectFeatureTransRect}
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 \alias{selectFeatureTransRect}
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-\title{Title Select features for a tensor generated from two matrices that
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+\title{Select features for a tensor generated from two matrices that
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  share samples.}
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 \usage{
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 selectFeatureTransRect(
... ... 
@@ -10,7 +10,7 @@ selectFeatureTransRect(
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   cond,
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   de = rep(1e-04, 2),
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   p0 = 0.01,
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-  breaks = 100,
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+  breaks = as.integer(100),
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   input_all = NULL
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 )
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 }
... ... 
@@ -33,7 +33,7 @@ list of logical vector that represent if the individual features
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 are selected and P-values.
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 }
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 \description{
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-Title Select features for a tensor generated from two matrices that
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+Select features for a tensor generated from two matrices that
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  share samples.
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 }
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 \examples{
... ... 
@@ -41,7 +41,7 @@ require(TDbasedUFE)
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 matrix1 <- matrix(runif(10000),200) #row features, column samples
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 matrix2 <- matrix(runif(20000),400) #row features, column samples
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 Z <- prepareTensorfromMatrix(t(matrix1),t(matrix2))
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-Z <- PrepareSummarizedExperimentTensorRect(sample=as.character(seq_len(50)),
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+Z <- prepareSummarizedExperimentTensorRect(sample=as.character(seq_len(50)),
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 feature=list(as.character(seq_len(200)),as.character(seq_len(400))),
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 sampleData=list(rep(seq_len(2),each=25)),value=Z)
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 HOSVD <- computeHosvd(Z)
Browse code

v-0.99.3

tagtag authored on 07/03/2023 15:02:58
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ 8bf7ddb
... ... 
@@ -2,7 +2,7 @@
2 2 
 % Please edit documentation in R/selectFeatureTransRect.R
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 \name{selectFeatureTransRect}
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 \alias{selectFeatureTransRect}
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-\title{Title Select features for a tensor generated from two matricies that
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+\title{Title Select features for a tensor generated from two matrices that
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  share samples.}
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 \usage{
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 selectFeatureTransRect(
... ... 
@@ -23,7 +23,7 @@ selectFeatureTransRect(
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 \item{p0}{threshold value for the significance}
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-\item{breaks}{number of bins of the histgram of P-values}
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+\item{breaks}{number of bins of the histogram of P-values}
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 \item{input_all}{The selected singular value vectors attributed to samples.
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 if NULL, interactive mode}
... ... 
@@ -33,7 +33,7 @@ list of logical vector that represent if the individual features
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 are selected and P-values.
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 }
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 \description{
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-Title Select features for a tensor generated from two matricies that
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+Title Select features for a tensor generated from two matrices that
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  share samples.
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 }
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 \examples{
Browse code

Futher addition after devtools:check() and BiocCheck

tagtag authored on 30/01/2023 13:07:17
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ bf055de
... ... 
@@ -41,9 +41,9 @@ require(TDbasedUFE)
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 matrix1 <- matrix(runif(10000),200) #row features, column samples
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 matrix2 <- matrix(runif(20000),400) #row features, column samples
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 Z <- prepareTensorfromMatrix(t(matrix1),t(matrix2))
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-Z <- PrepareSummarizedExperimentTensorRect(sample=as.character(1:50),
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-feature=list(as.character(1:200),as.character(1:400)),
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-sampleData=list(rep(1:2,each=25)),value=Z)
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+Z <- PrepareSummarizedExperimentTensorRect(sample=as.character(seq_len(50)),
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+feature=list(as.character(seq_len(200)),as.character(seq_len(400))),
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+sampleData=list(rep(seq_len(2),each=25)),value=Z)
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 HOSVD <- computeHosvd(Z)
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 cond <- list(attr(Z,"sampleData")[[1]],NULL,NULL)
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 index_all <- selectFeatureTransRect(HOSVD,cond,de=c(0.01,0.01),input_all=2)
Browse code

Correction based upon devttools::check()

tagtag authored on 29/01/2023 14:36:29
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ 3543352
... ... 
@@ -37,6 +37,7 @@ Title Select features for a tensor generated from two matricies that
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  share samples.
38 38 
 }
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 \examples{
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+require(TDbasedUFE)
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 matrix1 <- matrix(runif(10000),200) #row features, column samples
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 matrix2 <- matrix(runif(20000),400) #row features, column samples
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 Z <- prepareTensorfromMatrix(t(matrix1),t(matrix2))
Browse code

Tensor from matiricies that share samples

tagtag authored on 29/01/2023 13:11:31
Showing 1 changed files
man/selectFeatureTransRect.Rd
History View file @ ce756c8
1 1 
new file mode 100644
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@@ -0,0 +1,49 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/selectFeatureTransRect.R
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+\name{selectFeatureTransRect}
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+\alias{selectFeatureTransRect}
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+\title{Title Select features for a tensor generated from two matricies that
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+ share samples.}
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+\usage{
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+selectFeatureTransRect(
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+  HOSVD,
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+  cond,
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+  de = rep(1e-04, 2),
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+  p0 = 0.01,
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+  breaks = 100,
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+  input_all = NULL
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+)
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+}
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+\arguments{
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+\item{HOSVD}{HOSVD}
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+
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+\item{cond}{list of conditions}
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+
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+\item{de}{initial values for optimization of standard deviation}
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+
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+\item{p0}{threshold value for the significance}
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+
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+\item{breaks}{number of bins of the histgram of P-values}
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+
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+\item{input_all}{The selected singular value vectors attributed to samples.
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+if NULL, interactive mode}
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+}
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+\value{
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+list of logical vector that represent if the individual features
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+are selected and P-values.
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+}
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+\description{
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+Title Select features for a tensor generated from two matricies that
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+ share samples.
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+}
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+\examples{
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+matrix1 <- matrix(runif(10000),200) #row features, column samples
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+matrix2 <- matrix(runif(20000),400) #row features, column samples
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+Z <- prepareTensorfromMatrix(t(matrix1),t(matrix2))
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+Z <- PrepareSummarizedExperimentTensorRect(sample=as.character(1:50),
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+feature=list(as.character(1:200),as.character(1:400)),
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+sampleData=list(rep(1:2,each=25)),value=Z)
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+HOSVD <- computeHosvd(Z)
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+cond <- list(attr(Z,"sampleData")[[1]],NULL,NULL)
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+index_all <- selectFeatureTransRect(HOSVD,cond,de=c(0.01,0.01),input_all=2)
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+}