MissingHelpers: compute group mean by LOD

In wolski/prolfqua: Proteomics Label Free Quantification

compute group mean by LOD

Description

compute group mean by LOD

compute group mean by LOD

Details

weight lod by nr of NA's $(LOD * nrNas + meanAbundance *nrObs)/(nrMeasured)$

Public fields

data

data

config

config

prob

quantile of groups with one observed value to estimate LOD

stats

data.frame with group statistics

weighted

should we weight the LOD

Methods

Public methods

• MissingHelpers$new()

• MissingHelpers$get_stats()

• MissingHelpers$get_LOD()

• MissingHelpers$impute_weighted_lod()

• MissingHelpers$impute_lod()

• MissingHelpers$get_poolvar()

• MissingHelpers$get_contrast_estimates()

• MissingHelpers$get_contrasts()

• MissingHelpers$clone()

---

Method new()

initialize

Usage

MissingHelpers$new(data, config, prob = 0.5, weighted = TRUE)

Arguments

data

data

config

config

prob

default 0.5, median of groups with one observed value

weighted

should group average be computed used weighting, default TRUE.

---

Method get_stats()

get data.frame with statistics

Usage

MissingHelpers$get_stats()

Returns

data.frame

---

Method get_LOD()

determine limit of detection computes quantile of abundances in groups with a single observation

Usage

MissingHelpers$get_LOD()

Returns

integer LOD

---

Method impute_weighted_lod()

compute group averages using weighted lod

Usage

MissingHelpers$impute_weighted_lod()

---

Method impute_lod()

if group average absent substitute with LOD

Usage

MissingHelpers$impute_lod()

---

Method get_poolvar()

compute pooled var per protein

Usage

MissingHelpers$get_poolvar(prob = 0.75)

Arguments

prob

prob of sd from proteins where it can be computed

---

Method get_contrast_estimates()

get contrast estimates

Usage

MissingHelpers$get_contrast_estimates(Contrasts)

Arguments

Contrasts

named array with contrasts

---

Method get_contrasts()

compute contrasts

Usage

MissingHelpers$get_contrasts(Contrasts, confint = 0.95, all = FALSE)

Arguments

Contrasts

vector with contrasts

confint

compute confint

all

return all columns, default FALSE

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MissingHelpers$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

Contrasts <- c("group.b-a" = "group_A - group_B", "group.a-ctrl" = "group_A - group_Ctrl")
dd <- prolfqua::sim_lfq_data_protein_config(Nprot = 100,weight_missing = 2)
mh <- prolfqua::MissingHelpers$new(dd$data, dd$config, prob = 0.8,weighted = TRUE)
xx <- mh$get_stats()
xx <- mh$get_LOD()
xx <- mh$impute_weighted_lod()
xx <- mh$impute_lod()
xx <- mh$get_poolvar()
bb <- mh$get_contrast_estimates(Contrasts)
mh$get_contrasts(Contrasts)

dd <- prolfqua::sim_lfq_data_2Factor_config(Nprot = 100,weight_missing = 0.1)

Contrasts <- c("c1" = "TreatmentA - TreatmentB",
               "C2" = "BackgroundX- BackgroundZ",
               "c3" = "`TreatmentA:BackgroundX` - `TreatmentA:BackgroundZ`",
               "c4" = "`TreatmentB:BackgroundX` - `TreatmentB:BackgroundZ`"
               )
mh <- prolfqua::MissingHelpers$new(dd$data, dd$config, prob = 0.8,weighted = TRUE)
mh$get_stats()$interaction |> table()
mh$get_contrast_estimates(Contrasts)

wolski/prolfqua documentation built on Sept. 7, 2024, 3:06 a.m.