Nothing
context('results: missing value')
test_that('missingval_result correctly counts missing values', {
# Load data and create omicsData objects ---------------------------------------
load(system.file('testdata',
'little_pdata.RData',
package = 'pmartR'
))
# Create a pepData object with the reduced data set.
pdata <- as.pepData(
e_data = edata,
f_data = fdata,
e_meta = emeta,
edata_cname = "Mass_Tag_ID",
fdata_cname = "SampleID",
emeta_cname = "Protein"
)
# Create standards -----------------------------------------------------------
# Create rowwise counts.
count_row <- rowSums(is.na(pdata$e_data[, -1]))
# Create columnwise counts.
count_col <- colSums(is.na(pdata$e_data[, -1]))
# Create standard for naRes object.
standard <- list(
"na.by.sample" = data.frame("SampleID" = names(pdata$e_data)[-1],
"num_NA" = as.numeric(count_col),
"num_non_NA" = nrow(pdata$e_data) - as.numeric(count_col),
"Condition" = pdata$f_data[, 2]),
"na.by.molecule" = data.frame("Mass_Tag_ID" = pdata$e_data[, 1],
"num_NA" = as.numeric(count_row),
"num_non_NA" = nrow(pdata$f_data) - as.numeric(count_row)
)
)
# Add class and attribute crap to the standard.
class(standard) <- "naRes"
attr(standard, "cnames") <- list(
"edata_cname" = get_edata_cname(pdata),
"fdata_cname" = get_fdata_cname(pdata)
)
# Missing values: pepData object ---------------------------------------------
# Create an naRes object.
missingval <- missingval_result(pdata)
# Sleuth around the naRes object.
expect_identical(standard, missingval)
})
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