NEWS.md

In LDlinkR: Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

LDlinkR 1.4.0

• Added Zenodo DOI badge in version 1.3.0.9000
• 3/1/2024 - Increased maximum allowed variants in LDmatrix to 2500
• 3/1/2024 - Added bp window size parameter to LDproxy
• 3/4/2024 - Add bp window size parameter to LDproxy_batch

LDlinkR 1.3.0.9000 (development version)

• Add Zenodo DOI badge
• To do: Increase maximum allowed variants in LDmatrix to 3000.

LDlinkR 1.3.0

• Change LDlink Domain URL to https://ldlink.nih.gov/ (previous url root will no longer work following an unspecified amount of time).
• Add Continuous Integration using Github Actions.
• Update citation file with bibentry style

LDlinkR 1.2.3

• Add feature to provide root URL to API
• Fix bug that scrambled columns in LDproxy_batch when 'append' option is TRUE
• Update Roxygen version to 7.2.2

LDlinkR 1.2.2

• Issue #19, fix bug in LDtrait error handling of response data.
• Update CRAN downloads badge in README
• Remove link for 1000 Genomes Project in README and vignette

LDlinkR 1.2.1

• Update version number
• Fix bug in LDexpress that returned GRCH37 results when genome build was GRCh38 or GRCh38 High Coverage.
• Fix bug in LDproxy handling of error/warning messages in response data.
• Update RoxygenNote to 7.2.0

LDlinkR 1.2.0

• Submission date: 2022-05-11
• Issue #13 - Add new argument to LDhap (table_type) with four options for different types data output.
• Issue #14 - Fix LDhap valid input check for number of input 'snps', line 94.
• Add 'snps' to the WORDLIST
• Update test-ldhap with additional tests
• Update vignette with new LDhap usage examples with new argument.
• Make LDhap able to write to file for both types of data returned by the new 'table_type' options.
• Add feature 'genome_build' to support different genome builds, GRCh37(hg19), GRCh38(hg38), and GRCh38 High Coverage.
• Improve/update error and warning message returned in the response data from the LDlink API server.
• Fix CRAN note about 'LazyData' by removing line from Description file.
• Update README file.
• Add testthat tests for feature genome_build
• Add three new Illumina chips to SNPchip
• Add two new Affymetrix chips to SNPchip
• Major update to vignette with new feature genome_build

LDlinkR 1.1.2

• Submission date: 2021-02-19
• Add link to LDlink web site documentation.
• Correct code chunk in vignette FAQ #4, changed option to eval=FALSE; this vignette code chunk no longer requires an internet resource
• added notes to README and vignette that 'internet access required' to use
• Add code to check if required internet resources are available per CRAN

LDlinkR 1.1.1

• Release date: 2021-02-02
• Added three new functions, LDtrait, LDexpress & list_gtex_tissues
• Updated vignette with new descriptions of functions and examples.
• Major update to README.md, including basic examples
• Added a NEWS.md file to track changes to the package.
• Issue #2, fixed warning message from write.table in LDproxy_batch when append = TRUE
• Updated most function descriptions on package help page
• Added spell checking for building package

LDlinkR 1.0.2

• Release date 2020-03-02
• Minor updates

LDlinkR 1.0.1

• Release date 2019-10-17
• Minor updates made for publication.

LDlinkR 1.0.0

• Release date 2019-08-01
• Initial release.

LDlinkR documentation built on May 29, 2024, 4:32 a.m.