stats_minimal: The result of rifi_stats for artificial example data A...

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

The result of rifi_stats for artificial example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges and metadata (gff file processed, see gff file documentation)

Description

The result of rifi_stats for artificial example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges and metadata (gff file processed, see gff file documentation)

Usage

data(stats_minimal)

Format

A rowRanges of SummarizedExperiment with 24 rows and 45 variables:

ID:

The bin/probe specific ID

position:

The bin/probe specific position

intensity:

The relative intensity at time point 0

probe_TI:

An internal value to determine which fitting model is applied

flag:

Information on which fitting model is applied

position_segment:

The position based segment

delay:

The delay value of the bin/probe

half_life:

The half-life of the bin/probe

TI_termination_factor:

String, the factor of TI fragment

delay_fragment:

The delay fragment the bin belongs to

velocity_fragment:

The velocity value of the respective delay fragment

intercept:

The vintercept of fit through the respective delay fragment

slope:

The slope of the fit through the respective delay fragment

HL_fragment:

The half-life fragment the bin belongs to

HL_mean_fragment:

The mean half-life value of the respective half-life fragment

intensity_fragment:

The intensity fragment the bin belongs to

intensity_mean_fragment:

The mean intensity value of the respective intensity fragment

TU:

The overarching transcription unit

TI_termination_fragment:

The TI fragment the bin belongs to

TI_mean_termination_factor:

The mean termination factor of the respective TI fragment

seg_ID:

The combined ID of the fragment

pausing_site:

presence of pausing site indicated by +/-

iTSS_I:

presence of iTSS_I indicated by +/-

ps_ts_fragment:

The fragments involved in pausing site or iTSS_I

event_ps_itss_p_value_Ttest:

p_value of pausing site or iTSS_I

p_value_slope:

p_value of the slope

delay_frg_slope:

the slope value of the respective delay fragment

velocity_ratio:

Integer, ratio of velocity between 2 delay fragments

event_duration:

Integer, the duration between two delay fragments

event_position:

Integer, the position middle between 2 fragments with an event

FC_HL:

Integer, the fold change value of 2 HL fragments

FC_fragment_HL:

Integer, the fold change value of 2 intensity fragments

p_value_HL:

p_value of the fold change of HL fragments

FC_intensity:

Integer, the fold change value of 2 intensity fragments

FC_fragment_intensity:

String, fragments involved in fold change between 2 intensity fragments

p_value_intensity:

p_value of the fold change of intensity fragments

FC_HL_intensity:

ratio of fold change between 2 half-life fragments and fold change between 2 intensity 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_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:

Integer, the value correspomding to synthesis rate

synthesis_ratio_event:

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

p_value_Manova:

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

p_value_TI:

p_value of TI fragment

TI_fragments_p_value:

p_value of 2 TI fragments

Source

https://github.com/CyanolabFreiburg/rifi

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