filter_missval {DEP} | R Documentation

## Filter on missing values

### Description

`filter_missval` filters a proteomics dataset based on missing values. The dataset is filtered for proteins that have a maximum of 'thr' missing values in at least one condition.

### Usage

    filter_missval(se, thr = 0)

### Arguments

`se` | SummarizedExperiment, Proteomics data (output from `make_se()` or `make_se_parse()`).
`thr` | Integer(1), Sets the threshold for the allowed number of missing values in at least one condition.

### Value

A filtered SummarizedExperiment object.

### Examples

    # Load example
    data <- UbiLength
    data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
    data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

    # Make SummarizedExperiment
    columns <- grep("LFQ.", colnames(data_unique))
    exp_design <- UbiLength_ExpDesign
    se <- make_se(data_unique, columns, exp_design)

    # Filter
    stringent_filter <- filter_missval(se, thr = 0)
    less_stringent_filter <- filter_missval(se, thr = 1)

[Package DEP version 1.12.0 Index]