check_input: =========================================================================...

In CyanolabFreiburg/rifi: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

========================================================================= Check_input

Check_input reviews the input given by the user

Description

check_input stops the operation if the input data frame has severe faults. Less severe faults lead to the removal of wrong IDs and a warnings describing the problem. The Summarized Experiment colData must have the columns "timepoint" with the timepoints convertible to numeric and containing the timepoint 0. If replicates are used the column in colData must be called "replicate". The replicate must be convertible to numeric. In the RowRanges, optionally, IDs can be given as character (except ",","|","_"), but need to refer to a unique position/strand combination. Strand information needs to be given. The relative intensity in the assay must be numeric. The relative intensity for the first time point cannot be 0 or NA.

Usage

check_input(inp, thrsh = 0)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.
thrsh	numeric: the minimal allowed intensity for time point "0".

Value

the SummarizedExperiment object: checked, and with position, ID and filtration added to the rowRanges.

Examples

data(example_input_minimal)
check_input(inp = example_input_minimal, thrsh = 0)

CyanolabFreiburg/rifi documentation built on May 7, 2023, 7:53 p.m.