Table 1 Summary of various components of UPDG.
From: UPDG: U tilities package for data analysis of P ooled D NA G WAS
UPDG component | Function |
|---|---|
merge.pl | Combines genotype and intensity data of individual DNA GWAS from separate files |
adjustment.pl | Estimates allele frequencies of markers from DNA pools and performs adjustment correcting for allelic preferential amplification with the methods based on Hoogendoorn et al. (2000), Meaburn et al. (2006) and Craig et al. (2005), and generates input data files for the subsequent step of nested ANOVA |
QC.pl | Removes SNPs with minor allele frequencies and call rates below a user-specified threshold and generates filtered input data file for nested ANOVA |
nested_ANOVA_[H/M/N/U].r | Carries out nested ANOVA in R environment |
output_format.pl | Organizes results from nested ANOVA and generates a summary of markers with p values below a user-specified threshold |
mean_Rx_statistics.pl | Generates summary information on estimated allele frequencies for markers |