1. scmeth
  2. man
  3. cpgDensity.Rd
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updated the qcReport

Divyagash authored on 15/10/2018 11:08:10
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 3764abd
... ... 
@@ -29,7 +29,7 @@ of CpGs observed in certain base pair long region.
29 29 
 }
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 \examples{
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 library(BSgenome.Hsapiens.NCBI.GRCh38)
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-directory <- system.file("extdata/bismark_data",package='scmeth')
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+directory <- system.file("extdata/bismark_data", package='scmeth')
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 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
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-cpgDensity(bs,Hsapiens,1000,small=TRUE)
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+cpgDensity(bs, Hsapiens, 1000, small=TRUE)
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 }
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Removed dependency on dplyr

Divyagash authored on 20/03/2018 20:15:55
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 72433d7
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@@ -31,6 +31,5 @@ of CpGs observed in certain base pair long region.
31 31 
 library(BSgenome.Hsapiens.NCBI.GRCh38)
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 directory <- system.file("extdata/bismark_data",package='scmeth')
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 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
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-memory.limit(size=300)
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 cpgDensity(bs,Hsapiens,1000,small=TRUE)
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 }
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added additional option in cpgDensity function for small data sets

Divyagash authored on 20/03/2018 19:13:40
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 6a4a0d3
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@@ -5,7 +5,7 @@
5 5 
 \title{Provides Coverage by the CpG density. CpG Density is defined as the number
6 6 
 of CpGs observed in certain base pair long region.}
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 \usage{
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-cpgDensity(bs, organism, windowLength = 1000)
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+cpgDensity(bs, organism, windowLength = 1000, small = FALSE)
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 }
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 \arguments{
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 \item{bs}{bsseq object}
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@@ -13,7 +13,11 @@ cpgDensity(bs, organism, windowLength = 1000)
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 \item{organism}{scientific name of the organism of interest,
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 e.g. Mmusculus or Hsapiens}
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-\item{windowLength}{Length of the window to calculate the density
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+\item{windowLength}{Length of the window to calculate the density}
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+
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+\item{small}{Indicator for a small dataset, cpg density is calculated more
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+memory efficiently for large dataset but for small dataset a different quicker
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+method is used
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 Default value for window length is 1000 basepairs.}
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 }
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 \value{
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@@ -28,5 +32,5 @@ library(BSgenome.Hsapiens.NCBI.GRCh38)
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 directory <- system.file("extdata/bismark_data",package='scmeth')
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 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
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 memory.limit(size=300)
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-cpgDensity(bs,Hsapiens,1000)
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+cpgDensity(bs,Hsapiens,1000,small=TRUE)
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 }
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updated the man file for cpgDensity function

Divyagash authored on 19/03/2018 03:22:03
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 30276d5
... ... 
@@ -27,5 +27,6 @@ of CpGs observed in certain base pair long region.
27 27 
 library(BSgenome.Hsapiens.NCBI.GRCh38)
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 directory <- system.file("extdata/bismark_data",package='scmeth')
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 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
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+memory.limit(size=300)
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 cpgDensity(bs,Hsapiens,1000)
31 32 
 }
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Updated according to second review

Divyagash authored on 09/02/2018 22:42:04
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 1e49b4b
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@@ -11,7 +11,7 @@ cpgDensity(bs, organism, windowLength = 1000)
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 \item{bs}{bsseq object}
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 \item{organism}{scientific name of the organism of interest,
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-e.g. Mus musculus or Homo sapiens}
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+e.g. Mmusculus or Hsapiens}
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 \item{windowLength}{Length of the window to calculate the density
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 Default value for window length is 1000 basepairs.}
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Updated the files according to the review

Divyagash authored on 06/02/2018 16:16:57
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 69fbca4
... ... 
@@ -11,7 +11,7 @@ cpgDensity(bs, organism, windowLength = 1000)
11 11 
 \item{bs}{bsseq object}
12 12
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 \item{organism}{scientific name of the organism of interest,
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-i.e. Mus musculus or Homo sapiens}
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+e.g. Mus musculus or Homo sapiens}
15 15
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 \item{windowLength}{Length of the window to calculate the density
17 17 
 Default value for window length is 1000 basepairs.}
Browse code

Updated the package based on review comments.

Divyagash authored on 30/01/2018 16:00:41
Showing 1 changed files
man/cpgDensity.Rd
History View file @ be7d411
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@@ -2,7 +2,8 @@
2 2 
 % Please edit documentation in R/cpgDensity.R
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 \name{cpgDensity}
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 \alias{cpgDensity}
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-\title{Provides Coverage metrics in the repeat masker region}
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+\title{Provides Coverage by the CpG density. CpG Density is defined as the number
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+of CpGs observed in certain base pair long region.}
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 \usage{
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 cpgDensity(bs, organism, windowLength = 1000)
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 }
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@@ -12,17 +13,19 @@ cpgDensity(bs, organism, windowLength = 1000)
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 \item{organism}{scientific name of the organism of interest,
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 i.e. Mus musculus or Homo sapiens}
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-\item{windowLength}{Length of the window to calculate the density}
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+\item{windowLength}{Length of the window to calculate the density
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+Default value for window length is 1000 basepairs.}
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 }
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 \value{
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 Data frame with sample name and coverage in repeat masker regions
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 }
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 \description{
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-Provides Coverage metrics in the repeat masker region
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+Provides Coverage by the CpG density. CpG Density is defined as the number
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+of CpGs observed in certain base pair long region.
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 }
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 \examples{
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 library(BSgenome.Hsapiens.NCBI.GRCh38)
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-directory<-system.file("extdata/bismark_data",package='scmeth')
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-bs<-HDF5Array::loadHDF5SummarizedExperiment(directory)
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+directory <- system.file("extdata/bismark_data",package='scmeth')
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+bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)
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 cpgDensity(bs,Hsapiens,1000)
28 31 
 }
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Updated the extdata files to be compatible with new HDF5Array package

Divyagash authored on 23/01/2018 17:52:01
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 6fd96e9
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@@ -23,6 +23,6 @@ Provides Coverage metrics in the repeat masker region
23 23 
 \examples{
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 library(BSgenome.Hsapiens.NCBI.GRCh38)
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 directory<-system.file("extdata/bismark_data",package='scmeth')
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-bs<-SummarizedExperiment::loadHDF5SummarizedExperiment(directory)
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+bs<-HDF5Array::loadHDF5SummarizedExperiment(directory)
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 cpgDensity(bs,Hsapiens,1000)
28 28 
 }
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Updated the examples with bismark data

Divyagash authored on 18/09/2017 00:25:55
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 63f4f86
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@@ -21,7 +21,8 @@ Data frame with sample name and coverage in repeat masker regions
21 21 
 Provides Coverage metrics in the repeat masker region
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 }
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 \examples{
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-library(BSgenome.Mmusculus.UCSC.mm10)
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-load(system.file("extdata",'bsObject.rda',package='scmeth'))
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-cpgDensity(bs,Mmusculus,1000)
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+library(BSgenome.Hsapiens.NCBI.GRCh38)
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+directory<-system.file("extdata/bismark_data",package='scmeth')
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+bs<-SummarizedExperiment::loadHDF5SummarizedExperiment(directory)
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+cpgDensity(bs,Hsapiens,1000)
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 }
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Updated according to BiocCheck

Divyagash authored on 23/05/2017 01:08:18
Showing 1 changed files
man/cpgDensity.Rd
History View file @ ba93b44
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@@ -9,7 +9,8 @@ cpgDensity(bs, organism, windowLength = 1000)
9 9 
 \arguments{
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 \item{bs}{bsseq object}
11 11
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-\item{organism}{scientific name of the organism of interest, i.e. Mus musculus or Homo sapiens}
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+\item{organism}{scientific name of the organism of interest,
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+i.e. Mus musculus or Homo sapiens}
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 \item{windowLength}{Length of the window to calculate the density}
15 16 
 }
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added genomic build as an input for the functions

Divyagash authored on 18/05/2017 02:47:33
Showing 1 changed files
man/cpgDensity.Rd
History View file @ cb35657
... ... 
@@ -20,6 +20,7 @@ Data frame with sample name and coverage in repeat masker regions
20 20 
 Provides Coverage metrics in the repeat masker region
21 21 
 }
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 \examples{
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+library(BSgenome.Mmusculus.UCSC.mm10)
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 load(system.file("extdata",'bsObject.rda',package='scmeth'))
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-cpgDensity(bs,'Mus musculus',1000)
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+cpgDensity(bs,Mmusculus,1000)
25 26 
 }
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Added examples

Divyagash authored on 28/04/2017 21:46:39
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 5794d72
... ... 
@@ -20,5 +20,6 @@ Data frame with sample name and coverage in repeat masker regions
20 20 
 Provides Coverage metrics in the repeat masker region
21 21 
 }
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 \examples{
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-cpgDensity(bsseqObject,'Mus musculus',1000)
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+load(system.file("extdata",'bsObject.rda',package='scmeth'))
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+cpgDensity(bs,'Mus musculus',1000)
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 }
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Updated according to R CMD check

Divyagash authored on 25/04/2017 15:11:11
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 662e440
... ... 
@@ -11,7 +11,7 @@ cpgDensity(bs, organism, windowLength = 1000)
11 11
12 12 
 \item{organism}{scientific name of the organism of interest, i.e. Mus musculus or Homo sapiens}
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-\item{genome}{reference alignment, i.e. mm10 or hg38}
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+\item{windowLength}{Length of the window to calculate the density}
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 }
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 \value{
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 Data frame with sample name and coverage in repeat masker regions
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@@ -20,5 +20,5 @@ Data frame with sample name and coverage in repeat masker regions
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 Provides Coverage metrics in the repeat masker region
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 }
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 \examples{
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-repMask(bsseqObject,'Mus musculus','mm10')
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+cpgDensity(bsseqObject,'Mus musculus',1000)
24 24 
 }
Browse code

Added functions for the pheno Data of the bs object

Divyagash authored on 28/03/2017 15:08:04
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 77cf105
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@@ -4,7 +4,7 @@
4 4 
 \alias{cpgDensity}
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 \title{Provides Coverage metrics in the repeat masker region}
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 \usage{
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-cpgDensity(bs, organism, windowLength = 100)
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+cpgDensity(bs, organism, windowLength = 1000)
8 8 
 }
9 9 
 \arguments{
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 \item{bs}{bsseq object}
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Added the density

Divyagash authored on 08/03/2017 17:48:37
Showing 1 changed files
man/cpgDensity.Rd
History View file @ 0533306
1 1 
new file mode 100644
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@@ -0,0 +1,24 @@
1 
+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/cpgDensity.R
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+\name{cpgDensity}
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+\alias{cpgDensity}
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+\title{Provides Coverage metrics in the repeat masker region}
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+\usage{
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+cpgDensity(bs, organism, windowLength = 100)
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+}
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+\arguments{
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+\item{bs}{bsseq object}
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+
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+\item{organism}{scientific name of the organism of interest, i.e. Mus musculus or Homo sapiens}
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+
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+\item{genome}{reference alignment, i.e. mm10 or hg38}
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+}
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+\value{
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+Data frame with sample name and coverage in repeat masker regions
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+}
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+\description{
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+Provides Coverage metrics in the repeat masker region
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+}
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+\examples{
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+repMask(bsseqObject,'Mus musculus','mm10')
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+}