Man pages for cmcouto-silva/gt
Facilities for essential tasks in R
| admixture | ADMIXTURE |
| admixture.plot | Admixture Barplot |
| annotate_fromtbl | Annotate genes from a reference table |
| annot_snp_genes | Annotate Gene info from SNP ID |
| annovar | Annotate Genes |
| clean | Clean workspace |
| eigensoft2plink | Conversion from EIGEN to Plink format |
| flip_strand | Flip DNA strand |
| get_pca_outliers | Identify Outliers in PCA per group |
| get_snp_genes | Get Gene info from SNP ID |
| ggven_plot | Make a Tri Venn Diagram Plot |
| outlier | Identify outliers |
| pkg.lib | Load multiple packages in R |
| plink2eigensoft | Conversion from Plink to Eigenstrat format |
| plink_fst | Calculate Fst via Plink |
| plink_merge | Merge Plink files |
| plink_merge_list | Merge Multiple Plink files |
| plink_pca | Plink PCA analysis |
| plink.set.case.controls | Set cases and controls in .fam file from Plink |
| read.bim | Read bim file |
| read.vcf | Read vcf file |
| remove_monomorphic_alleles | Remove Monomorphic Alleles |
| reset_fam_state | Reset fam state from Plink |
| rm.extension | Remove file extension |
| see | Print first lines & columns from a data frame |
| separate_genes | Explode table based on genes |
| setFID | Set Family ID |
| shapeit_merge | Merge Shapeit files (.haps/.sample) |
| shapeit_set_ancestor | Adjust Ancentral/Derived Alleles According to Reference |
| shapeit_split | Split Shapeit files (.haps/.sample) |
| snpdata_mgmt | SNP Data Management |
| update_dist_genes | Remove annotation for SNPs distant grom genes |
| vcf_merge | Merge vcf files |
| write.bim | Write .bim |
| write.vcf | Write .vcf |
| xclip | Remove additional spaces/paragraphs from clipboard text |
