* FxCop is intended for class library developers. However, anyone creating applications that should comply with the .NET Framework best practices will benefit. FxCop is also useful as an educational tool for people who are new to the .NET Framework or who are unfamiliar with the .NET Framework Design Guidelines. * FxCop is designed to be fully integrated into the software development cycle and is distributed as both a fully featured application that has a graphical user interface (FxCop.exe) for interactive work, and a command-line tool (FxCopCmd.exe) suited for use as part of automated build processes or integrated with Microsoft Visual Studio® .NET as an external tool.

* Below are some examples of analyses that can be run in PLATO and the options that are available to the user. These examples are intended as a jumping off point for the user to customize their own analyses. For a handy list of all available commands and options, organized by function, see the PLATO Quick Reference, which lists the commands by function and is cross-referenced to their location in the manual. * Recode PED/MAP to Binary PLINK format $ plato load-data --file geno output-bed --file binarygeno * Recode Binary PLINK to PED/MAP, Only a Single Chromosome $ plato load-data --bfile bingeno --chrom 22 \ output-ped --ped geno.ped --map custom_geno.map * Perform a Simple Case/Control GWAS (no covariates, Bonferroni corrected p-values) $ plato load-data --bfile bingeno \ logistic --correction Bonferroni * PheWAS on Quantitative Outcomes using Markers with MAF between 10% and 40% $ plato load-data --bfile bingeno \ load-trait --file pheno.txt --missing=”-999” \ filter-maf --min 0.1 --max 0.4 linear --phewas --covariates AGE,BMI * EWAS (No Genetic Data, Quantitative Predictor Variables) $ plato load-trait --file pheno.txt --dummy-samples --extra-samples logistic --exclude-markers --use-traits --outcome PHENO * Concordance Checking (VCF vs. PED/MAP w/o FID) $ plato load-data --vcf-file data.vcf.gz concordance --file geno --no-fid * GWAS with Dog Data and Permutation Testing $ plato --chroms 38 load-data --file dog_geno logistic --permutations 1000