res_minimal: The result of event_dataframe for E.coli artificial example....

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

The result of event_dataframe for E.coli artificial example. A data frame combining the processed genome annotation and a SummarizedExperiment data from rifi_stats. The dataframe is

Description

The result of event_dataframe for E.coli artificial example. A data frame combining the processed genome annotation and a SummarizedExperiment data from rifi_stats. The dataframe is

Usage

data(res_minimal)

Format

A list with 2 items:

region:

the region from the gff file

gene:

String, gene annotation covering the fragments

locus_tag:

String, locus_tag annotation covering the fragments

strand:

the strand of the annotation

TU:

The overarching transcription unit

position:

The bin/probe specific position

FC_fragment_intensity:

String, fragments involved in fold change between 2 intensity fragments

FC_intensity:

Integer, the fold change value of 2 intensity fragments

p_value_intensity:

p_value of the fold change of intensity fragments

FC_fragment_HL:

Integer, the fold change value of 2 intensity fragments

FC_HL:

Integer, the fold change value of 2 HL fragments

p_value_HL:

p_value of the fold change of HL fragments

FC_HL_intensity_fragment:

fragments involved on ratio of fold change between 2 half-life fragments and fold change between 2 intensity fragments

FC_HL_intensity:

ratio of fold change between 2 half-life fragments and fold change between 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

p_value_Manova:

p_value of the variance between two fold-changes, HL and 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:

presence of pausing site indicated by +/-

iTSS_I:

presence of iTSS_I indicated by +/-

event_ps_itss_p_value_Ttest:

p_value of pausing site or iTSS_I

ps_ts_fragment:

The fragments involved in pausing site 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_frg_slope:

the slope value of the respective delay fragment

p_value_slope:

p_value of the slope

delay:

The delay value of the bin/probe

half_life:

The half-life of the bin/probe

intensity:

The relative intensity at time point 0

Source

https://github.com/CyanolabFreiburg/rifi

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