NEWS
IPCAPS 1.1.8 (2021-01-25)
Updates
- Updated the package according to R v4.0.2
- Reduce the sizes of example files
IPCAPS 1.1.7
Updates
- 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.
IPCAPS 1.1.6
Updates
- Corrected descripton of export.gorups
IPCAPS 1.1.5 (2018-06-14)
Updates
- 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
IPCAPS 1.1.4
Updates
- Added references in the DESCRIPTION file
- Added single quotes for Software's names in the DESCRRIPTION file
IPCAPS 1.1.3
Fixed Text
- In DESCRIPTION
- In README.Rmd
IPCAPS 1.1.2
Fixed Bugs
- Removed all examples for roxygen2 for all internal functions
- Removed all "library(IPCAPS)" in unit tests and examples
Changes
- All example files were changed from
simSNP*
to IPCAPS_example*
Added example file
- inst/extdata/IPCAPS_example.RData to used in the example of ipcaps()
IPCAPS 1.1.1
Added unit testing
- testthat/test_clusteringmode.R
Changes
- moved the nested functions in pasre.categorical.data and preprocess to parallelization.R
- add roxygen2 code to pasre.categorical.data, replace.missing, do.glm
Updates
- In roxygen part, changed from getwd() to tempdir()
- fixed errors according to check as cran
Fixed functions
- preprocess(): changed filename.label to label.file
IPCAPS 1.1.0
Updated functions
- 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.
IPCAPS 1.0.7
Added data
- 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
Added R file to describe data files
Added unit testing
- testthat/test_caleigenfit.R
- testthat/test_checkstopping.R
IPCAPS 1.0.6
Fixed functions
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
IPCAPS 1.0.5
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
IPCAPS 1.0.4.0
Fixed functions and objects
Removed the old RD files and added roxygen script to create manual for these
functions and objects:
IPCAPS-package
ipcaps
output.template
postprocess
IPCAPS 1.0.3.0
Fixed functions
Removed the old RD files and added roxygen script to create manual for these functions:
diff.eigen.fit
diff.xy
export.groups
get.node.info
IPCAPS 1.0.2.0
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
IPCAPS 1.0.1
Fixed functions
Removed the old RD files and added roxygen script to create manual for these functions:
cal.pc.linear
cal.pc.linear
cal.pc.linear
cal.pc.linear
IPCAPS 1.0.0.0
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
.