leqtar: Leqtar
In ErikSchutte/leqtar: Linear eQTL analysis in R

Description Usage Arguments Note

Leqtar uses a linear regression models for eQTL analysis. It has a multitude of options, play around with the test data that is availble to get a good idea of your optimal settings. Leqtar tries to do much of the normal pre-processing work for you. Leqtar corrects sample differences, dimensions problems, 'cell' type differences and other things. Please note to always double check your results and if there are any issues, please refer to https://github.com/ErikSchutte/leqtar/issues. This is a work in progress, I expect there to be bugs.

leqtar(run_name = NULL, genotypeFile = NULL, phenotypeFile = NULL,
  useModel = "linear", genotypePositionFile = NULL,
  phenotypePositionFile = NULL, covariateFile = NULL, geneNames = NULL,
  output_dir = NULL, genoToFreq = FALSE, forceRun = FALSE)

`run_name`	[REQUIRED] - A name that will be used for the current 'run'. This name has to be unique to perserve data, if you want to overwrite a run see 'forceRun'.
`genotypeFile`	[REQUIRED] - A Genotype file. SNP names are expected as colnames and sample names as rownames.
`phenotypeFile`	[REQUIRED] - A Phenotype file. Sample names are expected as colnames and stimulations/genes as rownames.
`useModel`	[REQUIRED] - A model used for QTL analysis. This can be 'linear', 'anova' or 'linear_cross'. This defaults to the 'linear' model.
`genotypePositionFile`	[OPTIONAL] - A file containing the positions for each SNP. The colnames are 'snp', 'chr' and 'pos'.
`phenotypePositionFile`	[OPTIONAL] - A file containing the positions for each gene.
`covariateFile`	[OPTIONAL] - A Covariate file containing covariates. Sample names are expected as colnames and covariates as rownames.
`geneNames`	[OPTIONAL] - A file containing the gene names that corrospond to Ensemble ID's or any other ID.
`output_dir`	[OPTIONAL] - A relative path from your current working directory or an absolute path to a specific directory. The results will be stored in this location. This defaults to your current working directory.
`genoToFreq`	[OPTIONAL] - Turns on conversion from genotypes i.e. 'AC' to a frequency for linear regression analysis. The default is set to 'FALSE'.
`forceRun`	[OPTIONAL] - Normally Leqtar perserves data, by turning this to ‘TRUE' runs that already exist will be overwritten. The default is set to ’FALSE'.