plink_pca: Plink PCA analysis
In cmcouto-silva/gt: Facilities for essential tasks in R

Plink PCA analysis

plink_pca(
  input,
  output,
  pop,
  col,
  iid_col,
  pop_col,
  ell_col,
  ld = c(50, 5, 0.5),
  pc.x = c(2, 3, 4, 3, 4, 4),
  pc.y = c(1, 1, 1, 2, 2, 3),
  k,
  track_iid = F,
  track_outlier = F,
  plot = T,
  plot_type = "png"
)

`input`	Character. The name (and path) of the plink binary files without extension.
`output`	Character. The prefix name for the output files.
`pop`	Optional. Data.frame or data.table containing the first two columns of the fam file (named as FID and IID, respectively), and additional columns with desired information for grouping populations (color and/or ellipses).
`col`	Optional. A named vector containing color name/code for each population.
`iid_col`	Optional. Character. Column name of the pop data.frame/data.table indicating the target-individuals.
`pop_col`	Optional. Character. Column name of the pop data.frame/data.table indicating the target-populations.
`ell_col`	Optional. Character. Column name of the pop data.frame/data.table for plotting ellipses. These ellipses are normal confidence ellipses computed by 'stat_ellipse' function from 'ggplot2' package.
`ld`	Numeric vector of length = 3. Indicates the window, step size and correlation threshold for LD filter, respectively. Default set to c(50, 5, 05). Set it to NULL if no LD filter is desired.
`pc.x`	Numeric vector. PC IDs for plotting. Default set to c(2, 3, 4, 3, 4, 4).
`pc.y`	Numeric vector. PC IDs for plotting. Default set to c(1, 1, 1, 2, 2, 3).
`k`	Numeric. Max number of PCs to be combined as figures. Default set to the length of pc.x/pc.y
`track_iid`	Character vector. Target individuals to be mapped on plot. Default set to FALSE (none).
`track_outlier`	Logical. Should outlier individuals be tracked on the figures? Default set to FALSE.
`plot`	Logical. Should PCA figures be generated? Default set to TRUE.
`plot_type`	Character. File format for output figures (e.g. bmp, jpeg, png, tiff, or pdf). Default set to png.