library(devtools)
if(!system.file(package='BIGDAWGv2')){
devtools::install_github('mmariani123/BIDAWGv2')
}
library(BIGDAWGv2)
#Select your species:
Species <- 'dla'
#Select your input data:
Data <- BIGDAWGv2::lab_data
#Data <- BIGDAWGv2::akitaData
#Choose your loci of interest:
LociSet <- list('DRB1','DQA1')
#Set your output directory:
resultsDir <- '<path/to/output/dir>'
#Set your other parameters and run BIGDAWGv2:
bigdawg.results <- BIGDAWGv2(
Data = Data,
Species = Species,
HLA = FALSE,
Run.Tests = c('HWE', 'A'),
Loci.Set = LociSet, #Must be a list or will throw an error
Exon = c(1),
All.Pairwise = FALSE,
Trim = FALSE,
Res = 2,
EVS.rm = FALSE,
Missing = 2,
Strict.Bin = FALSE,
Cores.Lim = 1L,
Results.Dir = ResultsDir,
Return = TRUE,
Output = TRUE,
Merge.Output = FALSE,
Verbose = TRUE)
############################## NOTES ################################### ######################################################################## ######################################################################## ######################################################################## ########################################################################
BIGDAWGv2 Software in progress with Professor Richard Single PhD of the University of Vermont and Professor Steven Mack of the University of California San Francisco. R package for statistical analyses of highly polymorphic genetic systems (e.g. HLA genes), now incorporating various non-human species.
Original BIGDAWG software:
Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) doi:10.1016/j.humimm.2015.12.006. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) doi:10.1007/978-1-61779-842-9_14.
For more details, please visit http://tools.immunogenomics.org.
BIGDAWG version2 in progress with additions by Michael P. Mariani PhD and Richard Single PhD.
Updates for BIGDAWGv2:
Code in the main BIGDAWG(v2) function has been refactored somewhat to allow for more species. New, smaller, sub, functions have been created from the code in this file. The main new paramtere is "Species" which can be set to "hla" - human, 'dla' - dog, 'bla' - cow, and 'gla' - chicken.
The Hardy Weinburg test will be updated to run without specifying controls in the input data set as this should run regardless.
The amino anid analaysis functionality needed to be updated to allow for species selection, and specifically, the uption to create a new ExonProtAlign object for a new species has to be incorporated and updateable Just like the 'hla' Exon object (.rda) is updateable
.rda objects will be stored in the top-level 'data' folder. Files used internally by the program are stored in the 'extdata' folder.
Thus the new code will generate an 'UpdatePtnAlign.RData' object and store it for use when 'dla' (or another species) is selected for anlaysis.
Additionally functionality was created in the create_files_functions.R file in order to create prot (_prot.txt) and pGroup (_nom_p.txt) files for the dla and genes and dla overall respectively. This functionality is not included as part of BIGDAWGv2 but had to be created for both testing and to create the Exon object that was needed, e.g. for use with the AA test.
The general AA test update workflow stacked as follows: A-Exon_Ptn_Align_functions_dog.R --> A_wrapper.R --> A.R These scripts call on the updated A_support functions file.
To create/update the new dog dla exon object the following files had to be modified both to allow for the creation of a new .rda object (not just updating) and to allow for updating of said object for new species. This new/updated Exon .rda object is stored in the top-level data folder as mentioned above
ExonPtnAlign.Create is found in A_ExonPtnAlign_functions_dog.R just as it was found in the original A_ExonPthAlign_functions.R file. The new AlignObj.Create and former AlignObj.Update functions are also found in this file.
Labrador and Akita (dog/dla) test data sets will be included in BIGDAWGv2 internally.
Specifically, when going through the AminoAcid Analysis component for dog,
debug(A.wrapper)
the Check.Params function was modified to allow for multiple species conditions
the run hla_checks was reorganized given the need for multiple species now and a new run_dla_checks function was created
The more generic check_functions.R file was modified in some cases again to add additional cases for additional species, e.g. dog.
mult_set_dup_check function was put in its own file and this function was commented out when dealing with dla data in the main BIGDAWGv2.R file/function.
CheckAlleles commnented out in run_dla_checks.R can consider something similar for dog
The run_amino_acid_analysis function has been adapated for multiple species now
A_wrapper.R runs a variety of functions, e.g., ExonFilter(), that are found in A_support_functions.R
Exon.Filter() is found in A_support_functions.R, AlignmentFilter, Condense.EPL is found here too.
The other functions in A_support_functions.R are run in the A.R file.
Thus run_amino_acid_analysis() will run A_wrapper(), which will run ExonFilter(), Condense.EPL(), and A().
#####################################################
end_analysis() function in BIGDAWGv2 main:
Do we want to set a specific path here?
For the ExonPtnAlign_functions_dog.R file, added the Species parameter and output path to extdata + species for the functions contained therein.
Note system.file vs. package.file
Probably could clean up ExonPtnAlign.Create() function more after adjustments
Remember had to use truncated allele for dog right now, see the ALignMatrix in A_ExonPtnAlign_functions_dog.R
Is the release.txt file being stored in the right location?
A_ExonPtnAlign_functions_dog.R could probably just be kept as A_ExonPtnAlign_functions.R with the additional species switching functionality included
Consider Bengstrom's future batch tools as well.
Still need to remove 'browser' commands where needed
Need to finish dog unit test and vignette
Need to remove labData as it was replaced with lab_data
Note first commands in BIGDAWGv2: options(warn=-1) MainDir <- getwd() on.exit(setwd(MainDir), add = TRUE)
ExonPtnAlign_dla.obj vs UpdatePtnAlign_dla.RData