event_dataframe: =========================================================================...

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

========================================================================= event_dataframe

event_dataframe creates a dataframe only with events

Description

event_dataframe creates a dataframe connecting segments, events and the annotation.

Usage

event_dataframe(data, data_annotation)

Arguments

data	dataframe: the probe based data frame.
data_annotation	dataframe: the coordinates are extracted from gff3

Details

The functions used are:

position_function: adds the specific position of ps or iTSS event.

annotation_function_event: adds the events to the annotated genes.

annotation file needs to be supplied. Strand is indicated in case of stranded data The event_dataframe selects columns with statistical features. ID, position, strand and TU columns are required.

Value

A dataframe with unique intensity 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

position:

Integer, position of the bin/probe on the genome

segment:

String, the bin/probe segment on the genome

FC_fragment_intensity:

String, the fragments subjected to fold change

FC_intensity:

Integer, the fold change value of 2 intensity fragments

p_value_intensity:

Integer, p_value of the FC_intensity

FC_fragment_HL:

String, the fragments subjected to fold change

FC_HL:

Integer, the fold change value of 2 HL fragments

p_value_HL:

Integer, p_value of the FC_HL

FC_HL_FC_intensity_fragment:

String, fragments subjected to FC_HL/FC_intensity

FC_HL_FC_intensity:

Integer, the value of FC_HL/FC_intensity

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

p_value_manova:

Integer, p_value of the event FC_HL/FC_intensity

synthesis_ratio:

Integer, the value correspomding to synthesis rate

synthesis_ratio_event:

String, the event assigned by synthesis rate either Termination or iTSS

pausing_site:

Boolean, presence or absence of pausing_site event (ps)

iTSS_I:

Boolean, presence or absence of internal starting site event (iTSS_I)

ps_ts_fragment:

String, fragments involved on the event ps or iTSS_I

event_position:

Integer, the position middle between 2 fragments with an event

event_duration:

Integer, the duration between two delay fragments

delay:

Integer, the delay value of the bin/probe

half_life:

The half-life of the bin/probe

intensity:

The relative intensity at time point 0

delay_frg_slope:

Integer, the slope value of the fit through the respective delay fragment

p_value_slope:

Integer, the p_value added to the inp

Examples

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

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