summary.lineupdist: Summarize inter-individual distances

Description

Summarize the results of distee() or disteg(), with inter-individual distances between two sets of gene expression data.

Usage

# S3 method for lineupdist
summary(
  object,
  cutoff = NULL,
  dropmatches = TRUE,
  reorder = c("alignmatches", "bydistance", "no"),
  ...
)

Value

A list with two components: the distances summarized by row and the distances summarized by column.

For each individual, we calculate the minimum distance to others, next-smallest distance, the self-self distance, the mean and SD of the distances to others, and finally indicate the individual (or individuals) that is closest.

Arguments

object: Output of distee() or disteg().
cutoff: (Optional) Cutoff on correlation/distance, with rows in the results only being kept if the best distance/correlation is above this cutoff or the self-self result is not missing and is above this cutoff.
dropmatches: If TRUE, omit rows for which an individual's best match is itself.
reorder: If "bydistance", reorder rows by increasing distance (or decreasing correlation) to the best match and then by decreasing distance (or decreasing correlation) to self; if "alignmatches", group related errors together; if "no", leave as is.
...: Passed to base::print.data.frame().

Author

Karl W Broman, broman@wisc.edu

Examples

Run this code

data(expr1, expr2)

expr1 <- expr1[,1:500]
expr2 <- expr2[,1:500]

# distance as correlation
d <- distee(expr1, expr2, "cor")

# summary of potential problems
summary(d)