dataframe_summary_events: =========================================================================...

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

========================================================================= dataframe_summary_events

dataframe_summary_events creates one table with all events between the segments

Description

dataframe_summary_events creates one table with the following columns: event, features, p_value, event_position, event_duration, position, region, gene, locus_tag, strand, TU, segment_1, segment_2, length, velocity_ratio, FC_HL, FC_intensity, FC_HL/FC_intensity.

Usage

dataframe_summary_events(data, data_annotation)

Arguments

data	SummarizedExperiment: the input data frame with correct format.
data_annotation	dataframe: dataframe from processed gff3 file.

Value

event:

String, event type either pausing site, iTSS_I, iTSS_II, Termination, HL_event, Int_event, HL_Int_event and velocity_change

p_value:

Integer, p_value of the event

p_adjusted:

Integer, p_value adjusted

FC_HL:

Integer, the fold change value of 2 HL fragments

FC_intensity:

Integer, the fold change value of 2 intensity fragments

FC_HL_adapted:

Integer, the fold change of half-life/ fold change of intensity, position of the half-life fragment is adapted to intensity fragment

synthesis_ratio:

Fold change of half-life/ fold change of intensity

event_position:

Integer, the position middle between 2 fragments with an event

velocity_ratio:

Integer, ratio of velocity between 2 delay fragments

feature_type:

String, region annotation covering the fragments

gene:

String, gene annotation covering the fragments

locus_tag:

String, locus_tag annotation covering the fragments

strand:

Boolean. The bin/probe specific strand (+/-)

TU:

String, The overarching transcription unit

segment_1:

String, the first segment of the event, includes the segment, TU, delay fragment in case of ps or iTSS_I. The rest of the events include HL fragment and intensity fragment

segment_2:

String, same description as segment_1 but is the second fragment of the event

event_duration:

Integer, the difference (min) between 2 delay fragment when ps or iTSS_I happen

gap_fragments:

Integer, length in position (nt), calculated by the difference between the last position of the first fragment and the first position of the second fragment.

features:

Integer, number of fragements involved on the event

Examples

if(!require(SummarizedExperiment)){
suppressPackageStartupMessages(library(SummarizedExperiment))
}
data(stats_minimal)
dataframe_summary_events(data = stats_minimal, 
data_annotation = metadata(stats_minimal)$annot[[1]])
 

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