Analysis Configuration

Analysis Configuration — holds all table annotations, hierarchy definitions, factor definitions, and analysis parameters in a single flat object.

See also

Other configuration: INTERNAL_FUNCTIONS_BY_FAMILY, R6_extract_values(), complete_cases(), concrete_AnalysisConfiguration, make_interaction_column(), make_reduced_hierarchy_config(), sample_subset(), separate_factors(), separate_hierarchy(), setup_analysis(), spread_response_by_IsotopeLabel(), table_factors(), table_factors_size()

Public fields

sep

separator to use when uniting columns is necessary

fileName

column name of column containing raw file names

sampleName

(will be generated from factors or fileName)

normValue

optional column with normalization values (e.g., Creatinine)

isotopeLabel

which column contains the isotope label (e.g. heavy or light), or light only if LFQ.

ident_qValue

column name with identification QValues (smaller better)

ident_Score

column with identification score (larger better)

opt_rt

optional column with rt information

opt_mz

optional column with mz information

nr_children

optional column containing for instance the number of peptides

workIntensity

column which contains the intensities

is_response_transformed

are the intensities transformed for constant variance

bin_resp

column with encoded missing information

factors

Names of columns containing factors (annotations)

factorDepth

number of relevant factors (used by plotting functions etc)

hierarchy

list with columns describing the measurement hierarchy (i.e. protein peptide precursor fragment)

hierarchyDepth

At which depth do you want to model i.e. protein than 1

min_peptides_protein

minimum number of peptides per protein

Active bindings

table

deprecated, use config directly. Returns self for backwards compatibility.

parameter

deprecated, use config directly. Returns self for backwards compatibility.

Methods

Public methods

• AnalysisConfiguration$new()

• AnalysisConfiguration$set_response()

• AnalysisConfiguration$get_response()

• AnalysisConfiguration$pop_response()

• AnalysisConfiguration$factor_keys()

• AnalysisConfiguration$factor_keys_depth()

• AnalysisConfiguration$hierarchy_keys()

• AnalysisConfiguration$hierarchyKeys()

• AnalysisConfiguration$hierarchy_keys_depth()

• AnalysisConfiguration$hkeysDepth()

• AnalysisConfiguration$id_required()

• AnalysisConfiguration$id_vars()

• AnalysisConfiguration$value_vars()

• AnalysisConfiguration$annotation_vars()

• AnalysisConfiguration$clone()

---

Method new()

create AnalysisConfiguration

Usage

AnalysisConfiguration$new(
  analysisTableAnnotation = NULL,
  analysisParameter = NULL
)

Arguments

analysisTableAnnotation

optional, for backwards compatibility with old constructor

analysisParameter

optional, for backwards compatibility with old constructor

---

Method set_response()

Add name of intensity column

Usage

AnalysisConfiguration$set_response(colName)

Arguments

colName

name of intensity column

---

Method get_response()

Get name of working intensity column

Usage

AnalysisConfiguration$get_response()

---

Method pop_response()

Remove last name in array of working intensity column names

Usage

AnalysisConfiguration$pop_response()

---

Method factor_keys()

Get factor keys

Usage

AnalysisConfiguration$factor_keys()

Returns

array with keys

---

Method factor_keys_depth()

Get factor keys till factorDepth

Usage

AnalysisConfiguration$factor_keys_depth()

---

Method hierarchy_keys()

get hierarchy keys

Usage

AnalysisConfiguration$hierarchy_keys(rev = FALSE)

Arguments

rev

return in reverse order

Returns

array of column names

---

Method hierarchyKeys()

get hierarchy keys (deprecated alias for hierarchy_keys)

Usage

AnalysisConfiguration$hierarchyKeys(rev = FALSE)

Arguments

rev

return in reverse order

Returns

array of column names

---

Method hierarchy_keys_depth()

get hierarchy keys up to depth

Usage

AnalysisConfiguration$hierarchy_keys_depth(names = TRUE)

Arguments

names

if TRUE names only if FALSE key value pairs

Returns

array of column names

---

Method hkeysDepth()

get hierarchy keys up to depth (deprecated alias for hierarchy_keys_depth)

Usage

AnalysisConfiguration$hkeysDepth(names = TRUE)

Arguments

names

if TRUE names only if FALSE key value pairs

Returns

array of column names

---

Method id_required()

Id Columns which must be in the input data frame

Usage

AnalysisConfiguration$id_required()

Returns

character array

---

Method id_vars()

get names of columns annotating values (e.g. intensities)

Usage

AnalysisConfiguration$id_vars()

Returns

character array

---

Method value_vars()

get names of columns containing observations e.g. (intensity, qValue, mz or rt)

Usage

AnalysisConfiguration$value_vars()

---

Method annotation_vars()

get names of columns with sample annotations

Usage

AnalysisConfiguration$annotation_vars()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

AnalysisConfiguration$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

istar <- sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
config <- istar$config
stopifnot("AnalysisConfiguration" %in% class(config))
stopifnot(length(config$hierarchy_keys()) > 0)
stopifnot(length(config$factor_keys()) > 0)
stopifnot(length(config$get_response()) == 1)