diff --git a/man/qc_plink.Rd b/man/qc_plink.Rd index 7ef4d20..618847f 100644 --- a/man/qc_plink.Rd +++ b/man/qc_plink.Rd @@ -5,14 +5,14 @@ \title{Compute quality-control of genotyping array (PLINK format) using a rmarkdown template.} \usage{ qc_plink( - input_directory = NULL, + input_files = NULL, output_directory = NULL, cohort_name = "COHORT", output_file = paste0(cohort_name, "_QC.html"), array = NULL, callrate_samples = 0.95, callrate_snps = 0.95, - heterozygosity_treshold = 4, + heterozygosity_threshold = 4, maf_threshold = 0.01, hwe_pvalue = 1e-04, includes_relatives = FALSE, @@ -45,7 +45,7 @@ qc_plink( ) } \arguments{ -\item{input_directory}{A \code{character}. The path to the plink files. +\item{input_files}{A \code{character}. The path to the plink files. The path should contains the file name without the extension, i.e., without \verb{*.bed}, \verb{*.bim} or \verb{*.fam}.} \item{output_directory}{A \code{character}. The path to the output directory.} @@ -62,7 +62,7 @@ Default is \code{0.95}.} \item{callrate_snps}{A \code{numeric}. The call rate threshold for probes, under which probes are excluded. Default is \code{0.95}.} -\item{heterozygosity_treshold}{A \code{numeric}. The heterozygosity threshold for samples +\item{heterozygosity_threshold}{A \code{numeric}. The heterozygosity threshold for samples (number of standard deviation from the mean), under/above which samples are excluded. Default is \code{4}.}