Nothing
context("summary: trelliData edata and trelliData")
test_that("trelliData object summaries return the correct data frames", {
testthat::skip_on_cran()
##################
## MS/NMR TESTS ##
##################
# Load: peptide expression data-----------------------------------------------
load(system.file('testdata',
'little_pdata.RData',
package = 'pmartR'
))
# Generate omicsData and statRes: peptide expression data---------------------
# Add more classes to the fdata file
fdata$Condition <- c(rep("InfectionA", 5), rep("InfectionB", 4), rep("Mock", 3))
# Create omics data object
pepOmics <- as.pepData(
e_data = edata,
f_data = fdata,
e_meta = emeta,
edata_cname = "Mass_Tag_ID",
fdata_cname = "SampleID",
emeta_cname = "Protein"
)
# Create statRes object
pepOmics <- edata_transform(omicsData = pepOmics, data_scale = "log2")
pepOmics <- group_designation(omicsData = pepOmics, main_effects = c("Condition"))
pepOmics <- applyFilt(filter_object = imdanova_filter(omicsData = pepOmics), omicsData = pepOmics, min_nonmiss_anova = 2, remove_singleton_groups = FALSE)
pepOmics <- normalize_global(pepOmics, "subset_fn" = "all", "norm_fn" = "median", "apply_norm" = TRUE, "backtransform" = TRUE)
pepStat <- imd_anova(omicsData = pepOmics, test_method = "combined")
# Make pepTrelli objects
pepTrelli1 <- as.trelliData.edata(e_data = edata, edata_cname = "Mass_Tag_ID", omics_type = "pepData")
pepTrelli2 <- as.trelliData(omicsData = pepOmics)
pepTrelli3 <- as.trelliData(statRes = pepStat)
pepTrelli4 <- as.trelliData(omicsData = pepOmics, statRes = pepStat)
# Make each of the four objects
suppressWarnings({
pepSummary1 <- pepTrelli1 %>% summary()
})
suppressWarnings({
pepSummary2 <- pepTrelli2 %>% summary()
})
suppressWarnings({
pepSummary3 <- pepTrelli3 %>% summary()
})
suppressWarnings({
pepSummary4 <- pepTrelli4 %>% summary()
})
# Panel by each options
suppressWarnings({
pepSumEdata <- pepTrelli4 %>%
trelli_panel_by("Mass_Tag_ID") %>%
summary()
})
suppressWarnings({
pepSumFdata <- pepTrelli4 %>%
trelli_panel_by("SampleID") %>%
summary()
})
suppressWarnings({
pepSumEmeta <- pepTrelli4 %>%
trelli_panel_by("Ref_ID") %>%
summary()
})
# Test: summary of the trelliData objects-------------------------------------
# Test that each have the correct number of rows
expect_equal(5, nrow(pepSummary1))
expect_equal(8, nrow(pepSummary2))
expect_equal(2, nrow(pepSummary3))
expect_equal(12, nrow(pepSummary4))
expect_equal(4, nrow(pepSumEdata))
expect_equal(2, nrow(pepSumFdata))
expect_equal(6, nrow(pepSumEmeta))
###################
## RNA-SEQ TESTS ##
###################
# Load: seqData expression data-----------------------------------------------
load(system.file('testdata',
'little_seqdata.RData',
package = 'pmartR'
))
seqData_omics <- as.seqData(e_data = edata, f_data = fdata, edata_cname = "ID_REF", fdata_cname = "Samples")
seqData_omics <- group_designation(seqData_omics, main_effects = "Tissue")
seqData_omics <- applyFilt(filter_object = total_count_filter(omicsData = seqData_omics), omicsData = seqData_omics, min_count = 15)
seqData_stat <- diffexp_seq(omicsData = seqData_omics, method = "voom")
# Test: seqData expression data-----------------------------------------------
seqSummary <- as.trelliData(omicsData = seqData_omics, statRes = seqData_stat) %>% summary()
# No abundance plots should be suggested in summary
expect_true(any(grepl("abundance", seqSummary$Plot)) == FALSE)
})
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