which_2ndbest: Determine which individual has 2nd-smallest distance to each...
In lineup2: Lining Up Two Sets of Measurements

Description Usage Arguments Value See Also Examples

For each individual represented in a distance matrix, find the individual giving the 2nd-smallest entry (with NAs for individuals present in only the rows or only the columns).

1	which_2ndbest(d, dimension = c("row", "column"), get_min = TRUE)

`d`	A distance matrix
`dimension`	Whether to get the 2nd-best by row or by column
`get_min`	If TRUE, get the 2nd-minimum; if FALSE, get the 2nd-maximum

A vector with all distinct individuals, with the character string labels for the individuals giving the 2nd-smallest (or largest) value by row or column. We include all individuals so that the results are aligned with the results of get_self().

get_2ndbest(), get_self(), get_best(), which_best()

# align rows in the provided dataset, lineup2ex
aligned <- align_matrix_rows(lineup2ex$gastroc, lineup2ex$islet)
# find correlated columns
selected_genes <- (corr_betw_matrices(aligned[[1]], aligned[[2]], "paired") > 0.75)
# calculate correlation between rows
similarity <- corr_betw_matrices(t(lineup2ex$gastroc[,selected_genes]),
                                 t(lineup2ex$islet[,selected_genes]), "all")
# which sample gives second-biggest value by row
secbest_byrow <- which_2ndbest(similarity, get_min=FALSE)

# which sample gives second-biggest value by column
secbest_bycol <- which_2ndbest(similarity, get_min=FALSE, dimension="column")