In kridsadakorn/ipcaps.bioc: Iterative Pruning to Capture Population Structure

knitr::opts_chunk$set(echo = TRUE)

IPCAPS.BIOC 2.0.0

• change the example files in the package
• add the vignettes for SNP anslysis and supported input files
• add the new parameter "seed"
• the function ipcaps is able to accept 'linear data' by specifying data.type='linear'
• add the parameter 'silence' to the function ipcaps
• all .Rdata files are now saved as 'bzip2' to reduce the files
• change all codes in the directory 'testthat' to enable silence mode
• compressed all example files from .txt to .txt.gz, and fixed the codes accordingly

Before moving to Bioconductor

IPCAPS 1.1.7

• 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

• Corrected descripton of export.gorups

IPCAPS 1.1.5

• 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

• Added references in the DESCRIPTION file
• Added single quotes for Software's names in the DESCRRIPTION file

IPCAPS 1.1.3

Fixed Text in:

• 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

• 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

• R/data.R

Added unit testing

• testthat/test_caleigenfit.R
• testthat/test_checkstopping.R

IPCAPS 1.0.6

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

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

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

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

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

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.

kridsadakorn/ipcaps.bioc documentation built on Jan. 22, 2020, 11:18 p.m.