- Updated the package according to R v4.0.2
- Reduce the sizes of example files
- Updated the functions to support re-analysis when the result files are moved to another directory; top.discriminator, ipcaps.
- top.discriminator now accepts a percentile for filtering.
- Corrected descripton of export.gorups
- Added more details in roxygen part of ipcaps-package.R
- Fixed text according to comments from CRAN
- Updated README.md according to the changes above
- Added references in the DESCRIPTION file
- Added single quotes for Software’s names in the DESCRRIPTION file
*Fixed Text in DESCRIPTION and README.Rmd
- Removed all examples for roxygen2 for all internal functions
- Removed all “library(IPCAPS)” in unit tests and examples
- All example files were changed from
simSNP* to IPCAPS_example*
- Added example file in inst/extdata/IPCAPS_example.RData to used in the example of ipcaps()
- Added unit testing, testthat/test_clusteringmode.R
- Moved the nested functions in pasre.categorical.data and preprocess to parallelization.R
- Added roxygen2 code to pasre.categorical.data, replace.missing, do.glm
- In roxygen part, changed from getwd() to tempdir()
- Fixed errors according to check as cran
- Fixed function, preprocess(): changed filename.label to label.file
- In check.stopping(), changed from eigen.fit = max(eigen.fit.vec[1:2]) to eigen.fit = max(eigen.fit.vec). This change may affect clustering result.
* data/IPCAPS_example.RData
* inst/extdata/IPCAPS_example.bed
* inst/extdata/IPCAPS_example.bim
* inst/extdata/IPCAPS_example.fam
* inst/extdata/IPCAPS_example.individuals.txt
* inst/extdata/IPCAPS_example_PC10.txt
* inst/extdata/IPCAPS_example_rowVar_colInd.txt
* testthat/test_caleigenfit.R
* testthat/test_checkstopping.R
- Removed the old RD files and added roxygen script to create manual for these functions:
save.plots.cluster.html
save.plots.label.html
save.plots
top.discriminator
- Fixed functions, Removed the old RD files and added roxygen script to create manual for these functions:
preprocess
process.each.node
save.eigenplots
save.html
- Fixed functions and objects, removed the old RD files and added roxygen script to create manual for these functions and objects:
IPCAPS-package
ipcaps
.template
postprocess
- Fixed functions, eemoved the old RD files and added roxygen script to create manual for these functions:
diff.eigen.fit
diff.xy
export.groups
get.node.info
- Fixed functions, removed the old RD files and added roxygen script to create manual for these functions:
cal.eigen.fit
check.stopping
clustering.mode
clustering
- Fixed functions, removed the old RD files and added roxygen script to create manual for these functions:
cal.pc.linear
Initial functions
-
cal.pc.linear A function for linear principal component analysis (PCA)
-
fst.each.snp.hudson A function for fixation index (Fst) calculation for all SNPs between two groups.
-
fst.hudson A function for average fixation index (Fst) calculation between two groups.
-
plot3views A function to create scatter plots in three views.
-
read.bed Read the binary PLINK format (BED, BIM, and FAM)
-
rubikclust A function for unsupervised clustering to detect rough structures and outliers.
-
write.bed Write an list of SNP object to the binary PLINK format (BED, BIM, and FAM)
-
xxt A function for calculating matrix multipication between a matrix and its transpose for large data.
Initial R data
-
simsnp Synthetic dataset containing single nucleotide polymorphisms (SNP)
-
sample_labels Synthetic dataset containing population labels for the dataset simsnp.
Initial example files
-
example_SNP.bed Synthetic dataset containing single nucleotide polymorphisms (SNP) in binary format
-
example_SNP.bim Simulated SNP information
-
example_SNP.fam Simulated sample information
Updates
From the initial idea, some functions were changed their names:
- The name of function
cal.PC.linear was changed to cal.pc.linear.
- The name of function
plot.3views was changed to plot3views.
- The name of function
rubikClust was changed to rubikclust.
- The name of function
XXt was changed to xxt.