CHANGELOG.md

In takahirosuzuki1980/test: Motif Overrepresentation analysis for Illumina Methylation Arrays

Changelog

[1.3] - 2018-08-07

Added

• IMAGE motidf database (https://genome.cshlp.org/content/28/2/243.long)

Fixed

• probeID2position_EPIC.R was integrated to ProbeID2positon.R and deleted.
• Conversion of duplicated probeIDs to position is available. (ProbeID2positon.R)
• dependecy of packages was fixed.
• Date was removed from output file.

[1.4] - 2018-11-09

Added

• sampling option
• Output of aignificantly enriched motif plots to a directory

Fixed

• Numer of core to be used has been changed from 16 to 4.

[1.5.0] - 2019-10-05

Update

• Format of scripts was hanged to Roxygen format.

Added

• When using the sampling option, indicate it on standerd out
• Output DMPs
• lumiMethyNorm support idat files as input
• lumiMethyNorm returns a selDataMatrix object
• MotScr support data.frame as input
• getIdat2M function: get, normalize, and M-value conputation from GEO ID

Fixed

• Error with the case of DMR = 0/1

[1.5.1] - 2019-12-27

Fixed

• debug of probeID2position.R
• debug of seqExtract.R

[1.5.2] - 2020-05-11

Fixed

• add "force" option to lumiMethyNorm.R, which is inherited option from readEPIC

[1.5.3] - 2020-05-23

Updated

• add "set.seed" to stratSampling.R to fix the randomization

[1.5.4] - 2020-06-11

Updated

• singel data vs multiple data-compliant

[1.5.5] - 2020-08-24

Updated

• min.score paraneter of MachPWM is variable

takahirosuzuki1980/test documentation built on April 2, 2021, 11 a.m.