summary.lineupdist {lineup}

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 class 'lineupdist'
summary(
  object,
  cutoff = NULL,
  dropmatches = TRUE,
  reorder = c("alignmatches", "bydistance", "no"),
  ...
)

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().

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.

Author(s)

Karl W Broman, [e-mail]

See Also

pulldiag(), omitdiag(), distee(), disteg(), plot2dist(), plot.lineupdist()

Examples

data(expr1, expr2)



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

# summary of potential problems
summary(d)