xadmix (version 1.0.0)

admix_subset: Admixture Data Subsetting

Description

Subset function optimized for admixture data. Filters for the percentages of any number of ancestry (K) columns and prints progress. Also allows passing additional arguments to filter columns with.

Usage

admix_subset(
  data,
  anc = NULL,
  pct = NULL,
  comparison = "greater",
  quiet = FALSE,
  ...
)

Value

A subset of the provided data frame.

Arguments

data

Data frame containing the admixture data.

anc

Vector of ancestry column names to use for pairwise subsetting with percentage vector. Must be of same length as the supplied percentage vector.

pct

Vector of percentage values to use for pairwise subsetting with ancestry column name vector. Only ancestries with values above the percentage are kept.

comparison

What comparison operator to use for the subsetting. Can either be "greater" or "less"; default is "greater". Also accepts "gt", "lt", ">" and "<".

quiet

Whether to print progress or not; default is "FALSE".

...

Variable number of additional vectors for subsetting. Looking at the column with argument name, keeps only those observations with values which are elements of the argument vector.

Examples

# load simulated admixture data
data("xadmixture")

# keep only observations with K1 > 0.1 and K2 > 0.01
subset1 <- admix_subset(xadmixture, 
                        anc = c("K1", "K2"), 
                        pct = c(0.1, 0.01))

# keep only observations with K2 < 0.4 and K3 < 0.1
subset2 <- admix_subset(xadmixture, 
                        anc = c("K2", "K3"), 
                        pct = c(0.4, 0.1), 
                        comparison = "less")

# keep only observations with values "GBR" or "FRA" in column 
# "country" and values "lorem" or "dolor" in column "species"
subset3 <- admix_subset(xadmixture, 
                        country = c("GBR", "FRA"), 
                        species = c("lorem", "dolor"))

# keep only observations with K1 > 0.1 and K4 < 0.3, 
# without printing progress; subsets can be chained 
# using the pipe operator from package `magrittr` 
library(magrittr)
subset4 <- admix_subset(xadmixture, 
                        anc = "K1", 
                        pct = 0.1, 
                        quiet = TRUE) %>% 
 admix_subset(anc = "K4", 
              pct = 0.3, 
              comparison = "less", 
              quiet = TRUE)