AnnotationProcessor

AnnotationProcessor

AnnotationProcessor

Public fields

QC

is it a QC run

prefix

name for one factor designs

repeated

is it a repeated measurement

SAINT

is it a AP MS experiment, then use Bait_ as prefix

file_pattern

colnames for file

grouping_pattern

colnames grouping variable

subject_pattern

colnames for pairing variable

control_pattern

contrast specification columns

control_col_pattern

columns which contains C or T.

sample_name_pattern

sample name column

sample_name_suffix_length

maximum suffix length for display sample names

sample_name_display_column

preferred derived display sample-name column

shorten_sample_names

derive short display names for long sample names

norm_value_pattern

normalization value column (e.g., Creatinine)

strict

should name check be strict

Methods

Public methods

• AnnotationProcessor$new()

• AnnotationProcessor$check_annotation()

• AnnotationProcessor$read_annotation()

• AnnotationProcessor$extract_contrasts()

• AnnotationProcessor$add_contrasts_vec()

• AnnotationProcessor$clone()

---

Method new()

initialize

Usage

AnnotationProcessor$new(
  QC = FALSE,
  prefix = "G_",
  repeated = TRUE,
  SAINT = FALSE,
  shorten_sample_names = TRUE,
  sample_name_suffix_length = 14L,
  sample_name_display_column = "sampleName"
)

Arguments

QC

default FALSE

prefix

default "G_"

repeated

default TRUE

SAINT

default FALSE

shorten_sample_names

derive short display sample names from long names

sample_name_suffix_length

suffix length used for derived sample names

sample_name_display_column

preferred derived display sample-name column

---

Method check_annotation()

check annotation

Usage

AnnotationProcessor$check_annotation(annot)

Arguments

annot

annotation

---

Method read_annotation()

read annotation

Usage

AnnotationProcessor$read_annotation(dsf)

Arguments

dsf

either dataframe or file path.

---

Method extract_contrasts()

check annotation

Usage

AnnotationProcessor$extract_contrasts(annot, group)

Arguments

annot

annotation

group

group column e.g. group

---

Method add_contrasts_vec()

add vector of contrasts to annot table

Usage

AnnotationProcessor$add_contrasts_vec(annot, Contrasts)

Arguments

annot

annotation

Contrasts

vector with contrasts

---

Method clone()

The objects of this class are cloneable with this method.

Usage

AnnotationProcessor$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# AnnotationProcessor$debug("read_annotation")
ap <- AnnotationProcessor$new(prefix = "G_")

annot <- data.frame(
file = c("a1.raw","a2.raw","a3.raw","a4.raw"),
group = c("a","a","b","b"),
CONTROL = c("C","C","T","T"),
Subject = c("X","Y","X","Y"))
ap$check_annotation(annot)
#> Warning: column starting with :^name is missing.
af <- annot
af$file <- NULL
testthat::expect_error(ap$check_annotation(af), "column starting with :")
af <- annot
af$group <- NULL
testthat::expect_error(ap$check_annotation(af),"column starting with :")
#> Warning: column starting with :^name is missing.
aa <- ap$read_annotation(annot)
#> Warning: column starting with :^name is missing.
#> INFO [2026-06-23 20:42:34] levels: c("a", "b") c("C", "T")
#> b a 
stopifnot(length(aa$atable$factor_keys_depth()) == 2)
stopifnot(all(c("atable", "annot", "contrasts") %in% names(aa)))
stopifnot(aa$contrasts == "G_b - G_a")
af <- annot
af$CONTROL <- NULL
testthat::expect_error(ap$check_annotation(af),"you must specify a CONTROL column")
#> Warning: column starting with :^name is missing.
af <- annot
af$Subject <- NULL
testthat::expect_warning(ap$check_annotation(af),"column starting with")


# should not throw exception since QC does not require group or subject
ap <- AnnotationProcessor$new(QC = TRUE)
af <- annot
# af$group <- NULL
af$CONTROL <- NULL
af$Subject <- NULL
ap$check_annotation(af)
#> Warning: column starting with :^name is missing.
aa <- ap$read_annotation(af)
#> Warning: column starting with :^name is missing.

stopifnot(aa$atable$factor_keys() == "G_")
stopifnot(aa$atable$factors == "group")
aa <- ap$read_annotation(annot)
#> Warning: column starting with :^name is missing.
aa$atable$file_name
#> [1] "file"
aa$atable$sample_name
#> [1] "sampleName"
as <- annot
as$sample <- c("s1","s2","s3","s4")
aa <- ap$read_annotation(annot)
#> Warning: column starting with :^name is missing.
aa$atable$sample_name
#> [1] "sampleName"
stopifnot(is.null(aa$annotation))

annot <- data.frame(
file = c("a1.raw","a2.raw","a3.raw","a4.raw"),
Name = c("a1.raw","a2.raw","a3.raw","a4.raw"),
"Grouping Var" = c("a","a","b","b"),
CONTROL = c("C","C","T","T"),
Subject = c("X","Y","X","Y"))
ax <- ap$read_annotation(annot)