Description Usage Arguments Value See Also Examples
View source: R/which_2ndbest.R
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()
1 2 3 4 5 6 7 8 9 10 11 12 | # 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")
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