History.md

In PhHermann/LDJump: Estimating Variable Recombination Rates from Population Genetic Data

Source History

The most recent version of LDJump is 0.2.2 For installation of LDJump please see README.md and can be downloaded in this folder.

Update Version 0.1.1.

The functions LDJump and getSmuce are extended with a parameter constant. By default this is set to FALSE such that variable recombination rates are estimated. If set to TRUE, then a constant recombination rate is estimated for the whole sequence.

Update Version 0.1.2

The smuceR function to apply SMUCE is exchanged with the function stepFit due to the update of the stepR package and the notification that the first function might be removed in future updates. Moreover, a note due to package imports and dependencies has been fixed.

Update Version 0.1.3

We have changed several function calls due to package imports and dependencies in the previous version. We also updated the main function in order to be able to efficiently apply LDJump under a vector of type I error probabilities. Moreover, the output has more detailed descriptions. We also added an optional parameter to rescale the sequence length to the unit interval.

Update Version 0.1.4

Fixed minor bugs and paths to LDhat. Also an optional parameter is added which prints the current status of the calculated segment on screen. Example files are also updated.

Update Version 0.1.5

Added the option to impute recombination rates of segments having less than 2 SNPs. User input is required to continue the computation with LDJump.

Update Version 0.1.6

Fixed minor bug and added option to fgt_rrate_dpr.R.

Update Version 0.1.7

LDJump can now be applied in parallel on several cores. Therefore, an additional parameter is added to the command which reflects the integer number of cores on which the recombination map should be estimated.

Update Version 0.1.8

Thanks to user request we have added the option to ignore the user input in case of segments lacking SNPs. Moreover, slight adaptions to commands using the working directory were made.

Update Version 0.1.9

We have also simulated under demographic effects and provide a regression model for this setup. This is implemented via an logical parameter demography, which will use this regression model if the recombination rates should be estimated under demographic effects.

Update Version 0.1.10

Fix issues with paths. LDJump should be applied with the full path of the file containing the sequences (\code{seqName}). Moreover, the function impute was rewritten.

Update Version 0.2.1

We have implemented the function calcRegMod in order to estimate the regression function for constant estimates under simulated populations with a user input demographic scenario. This function requires the two software packages scrm and ms2dna to be installed. Therefore, we also included an optional parameter in the main function in oder to apply LDJump under the newly trained regression model.

We added the parameter out which enables to specify a string added to the output-files. Hence, it is not required anymore to run LDJump from different directories when applying it on several data sets in parallel.

Update Version 0.2.2

We updated the regression models for constant recombination rates in LDJump and therefore, also updated all other models such as the bias correction model or the demography model. These models are based on summary statistics computed from among others the software package PhiPack. The computing time of LDJump is reduced drastically. Additionally, one can still use LDhat in order to reduce the runtime of LDJump.

Update Version 0.3.1

In this update, we added an extension vcf_to_fasta which allows LDJump to receive and work with VCF-files. Because of this adjustment, major changes and debugging have been done in other functions of LDJump, such as LDJump, summary_statistics, vcfR_to_fasta. Additionally, a new function vcf_statistics has been created, which is the main working unit when using VCF-files. The new update also allows the user to parallelize and therefore shorten the running time when working with VCF-files.

PhHermann/LDJump documentation built on Nov. 16, 2019, 12:53 p.m.