Man pages for gziegler/ionomicsUtils
Utility functions for ionomics data analysis
| calcHet | Calculate fraction of hets for each SNP in a genotype table. |
| calcMAF | Takes a recoded (0,1,2) data.table and returns a two column... |
| eigenstrat | Calculate PCs similar to eigenstrat of genotype matrix |
| ionomicsUtils-package | Utility functions for ionomics data analysis |
| is.outlier | Remove outliers from the provided vector and return vector... |
| labelOutliers | Create a ggplot with outliers colored. |
| lm_eqn | Return a linear model equation with R^2 value |
| missingByLine | Takes a recoded (0,1,2) data.table and returns a single row... |
| multiplot | Multiple plot function |
| outlierRemoveDataset | Calls is.outlier for all of the data columns (cols) of the... |
| realizedAB | Calculate Astle-Balding Kinship using Synbreed Kinship... |
| recode | Takes a SNP vector and converts to 0,1,2 coding |
| recodeBiallele | Takes a biallelic SNP vector and converts to 0,1,2 coding |
| recodeGenoTable | Take a data.table genotype file and call 'recode' to convert... |
| scatterPlot | Make an ionomics scatter plot with points in order run on... |
| SymboltoElementName | Convert element symbol to full element name |
| visReps | Visualize where replicates occur in an ionomics run |
| weightEstimation | Predict weights of samples from ionomics data. |
