simplePHENOTYPES 1.2.4

Major changes

Input 1. Implemented options for input format as VCF, plink bed/ped files, GDS. 1. Changed dosage (numeric format) information from 0, 1, and 2 to -1 (aa), 0 (Aa) and 1 (AA). 1. Implemented a new type of spurious pleiotropy, direct LD (type_of_ld = “indirect”). 1. Included the option for assigning a residual correlation among traits. 1. Implemented a constrain option to select only heterozygote or only homozygote QTNs. 1. Included the warning_file_saver option to skip asking if the user wants to save one genotype file for each rep when vary_QTN = FALSE.

Output 1. Included a new output file with the summary linkage disequilibrium information on the selected spurious pleiotropy QTNs. 1. Included MAF in the outputted QTN information file. 1. Calculates the proportion of phenotypic variation explained by each QTN (QTN_variance = TRUE). 1. Includes the option to remove QTNs from the genotype file (remove_QTN = TRUE). 1. Renamed by in Tassel output format.

Minor changes

Fixed bug that didn’t recognize geno_obj as HapMap. Fixed bug when simulating dominance will all SNPs being homozygotes. Fixed bug when reaching the end of the file while looking for SNPs in LD. Fixed bug in importing geno_file from other directories. Fixed bug in selecting QTNs when marker data < 6 SNPs. Included file removal when simulation does not complete. Renamed file outputted as numeric. Renamed constrain option. Implemented check for biallelic markers. Changed the QTN file name. Implemented an interactive question before Check to remove QTNs with vary_QTN = T. Included check.names as FALSE in all data.frames. Check if geno_file and geno_path are NULL. Incorrect output name.