tests/testthat/test-checkAnnoArguments.R

In Rtpca: Thermal proximity co-aggregation with R

## Tests for .checkAnnoArguments
## library(Rtpca); library(testthat)
context(".checkAnnoArguments")

library(dplyr)
library(Biobase)

m1 <- matrix(1:12, ncol = 4)
m2 <- matrix(2:13, ncol = 4)
m3 <- matrix(c(2:10, 1:7), ncol = 4)

rownames(m1) <- 1:3
rownames(m2) <- 2:4
rownames(m3) <- 2:5

colnames(m1) <- paste0("X", 1:4)
colnames(m2) <- paste0("X", 1:4)
colnames(m3) <- paste0("X", 1:4)

mat_list <- list(
    m1, m2, m3
)

ppi_anno <- tibble(
    gene_name1 = "2",
    gene_name2 = "3",
    combined_score = 700,
    pair = "2:3")

tpcaTest1 <- .checkAnnoArguments(
    objList = mat_list,
    complexAnno = NULL,
    ppiAnno = ppi_anno
)

expect_s4_class(object = tpcaTest1, 
                class = "tpcaResult")

expect_error(
    .checkAnnoArguments(objList = mat_list),
    paste(c("Neither complex annotation nor a PPI", 
            "annotation were supplied!\n",
            "One of them is required."),
          collapse = " ")
)