LFQDataSummariser: Summarize LFQData

In wolski/prolfqua: Proteomics Label Free Quantification

Summarize LFQData

Description

Summarize LFQData

Summarize LFQData

Public fields

lfq

LFQData

Methods

Public methods

• LFQDataSummariser$new()

• LFQDataSummariser$hierarchy_counts()

• LFQDataSummariser$hierarchy_counts_sample()

• LFQDataSummariser$plot_hierarchy_counts_sample()

• LFQDataSummariser$interaction_missing_stats()

• LFQDataSummariser$upset_interaction_missing_stats()

• LFQDataSummariser$missingness_per_group()

• LFQDataSummariser$missingness_per_group_cumsum()

• LFQDataSummariser$plot_missingness_per_group()

• LFQDataSummariser$plot_missingness_per_group_cumsum()

• LFQDataSummariser$percentage_abundance()

• LFQDataSummariser$clone()

---

Method new()

initialize

Usage

LFQDataSummariser$new(lfqdata)

Arguments

lfqdata

LFQData

---

Method hierarchy_counts()

summarize hierarchy

Usage

LFQDataSummariser$hierarchy_counts()

---

Method hierarchy_counts_sample()

number of elements at each level in every sample

Usage

LFQDataSummariser$hierarchy_counts_sample(
  value = c("wide", "long"),
  nr_children = 1
)

Arguments

value

wide - wide format, long - long format, plot - ggplot

nr_children

get summary for 1,2 or more number of children

---

Method plot_hierarchy_counts_sample()

barplot showing number of elements at each level in every sample

Usage

LFQDataSummariser$plot_hierarchy_counts_sample(nr_children = 1)

Arguments

nr_children

get summary for 1,2 or more number of children

value

wide - wide format, long - long format, plot - ggplot

---

Method interaction_missing_stats()

missing per condition and protein

Usage

LFQDataSummariser$interaction_missing_stats()

---

Method upset_interaction_missing_stats()

upset plot with missing information per protein and condition

Usage

LFQDataSummariser$upset_interaction_missing_stats(tr = 2)

Arguments

tr

if less than tr observations in condition then missing

---

Method missingness_per_group()

missing stats per condition

Usage

LFQDataSummariser$missingness_per_group()

---

Method missingness_per_group_cumsum()

missing stats per condition as cumulative sum

Usage

LFQDataSummariser$missingness_per_group_cumsum()

---

Method plot_missingness_per_group()

barplot with number of features with 1,2, etc missing in condition

Usage

LFQDataSummariser$plot_missingness_per_group()

Returns

ggplot

---

Method plot_missingness_per_group_cumsum()

barplot with cumulative sum of features with 1,2, etc missing in condition

Usage

LFQDataSummariser$plot_missingness_per_group_cumsum()

Returns

ggplot

---

Method percentage_abundance()

Does roll up to highest hierarchy and Computes the percent abundance of proteins overall and within each group

Usage

LFQDataSummariser$percentage_abundance()

Returns

data frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

LFQDataSummariser$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

Other LFQData: LFQData, LFQDataAggregator, LFQDataPlotter, LFQDataStats, LFQDataToSummarizedExperiment(), LFQDataWriter, ProteinAnnotation

Examples

istar <- prolfqua::sim_lfq_data_peptide_config()

data <- istar$data
lfqdata <- LFQData$new(data, istar$config)
sum <- lfqdata$get_Summariser()
sum
sum$hierarchy_counts()
sum$hierarchy_counts_sample("wide")
sum$hierarchy_counts_sample("long")
sum$plot_hierarchy_counts_sample()
sum$plot_hierarchy_counts_sample()
tmp <- sum$interaction_missing_stats()

sum$missingness_per_group()
sum$missingness_per_group_cumsum()
sum$plot_missingness_per_group()
sum$plot_missingness_per_group_cumsum()
sum$upset_interaction_missing_stats()
sum$percentage_abundance()

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.