summary_e_coli: The result of rifi_summary for E.coli example data A...

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

The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges

Description

The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges

Usage

data(summary_e_coli)

Format

The rowRanges of SummarizedExperiment:

bin_df:

all information regarding bins:

ID:

The bin/probe specific ID

feature_type:

String, region annotation covering the fragments

gene:

String, gene annotation covering the fragments

locus_tag:

String, locus_tag annotation covering the fragments

position:

The bin/probe specific position

strand:

The bin/probe specific strand

segment:

The segment the bin/probe belongs to

TU:

The overarching transcription unit

delay_fragment:

The delay fragment the bin/probe belongs to

delay:

The delay of the bin/probe

HL_fragment:

The half-life fragment the bin/probe belongs to

half_life:

The half-life of the bin/probe

intensity_fragment:

The intensity fragment the bin/probe belongs to

intensity:

The relative intensity at time point 0

flag:

The flag of the bin/probe(TI, PDD)

TI_termination_factor:

String, the factor of TI fragment

frag_df:

all information regarding 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

first_position_frg:

The first position of the fragment on the genome

last_position_frg:

The last position of the fragment on the genome

strand:

The bin/probe specific strand

TU:

The overarching transcription unit

segment:

The segment the fragment belongs to

delay_fragment:

The delay fragment of the fragment

HL_fragment:

The half-life fragment of the fragment

half_life:

The half-life mean of the fragment

HL_SD:

The half-life standard deviation of the fragment

HL_SE:

The half-life standard error of the fragment

intensity_fragment:

The intensity_fragment of the fragment

intensity:

The relative intensity at time point 0

intensity_SD:

The intensity standard deviation of the fragment

intensity_SE:

The intensity standard error of the fragment

velocity:

The velocity value of the respective delay fragment

event_df:

all information regarding events:

event:

String, event type

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:

Fold change of 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

FC_HL_FC_intensity:

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:

The bin/probe specific strand

TU:

The overarching transcription unit

segment_1:

String, the first fragment of the two of fragments subjected to analysis

segment_2:

String, the second fragment of the two of fragments subjected to analysis

event_duration:

Integer, the duration between two delay fragments

gap_fragments:

Integer, the distance between two delay fragments

features:

Integer, number of fragements involved on the event

events_HL_int_df:

all information regarding events related to half-life and intensity:

event:

String, event type

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

FC_HL_FC_intensity:

Fold change of half-life/ fold change of intensity

event_position:

Integer, the position middle between 2 fragments with an event

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:

The bin/probe specific strand

TU:

The overarching transcription unit

segment_1:

String, the first fragment of the two of fragments subjected to analysis

segment_2:

String, the second fragment of the two of fragments subjected to analysis

event_duration:

Integer, the duration between two delay fragments

gap_fragments:

Integer, the distance between two delay fragments

features:

Integer, number of fragements involved on the event

events_ps_itss_df:

all information regarding events related to pausing sites and iTSS_I:

event:

String, event type

p_value:

Integer, p_value of the event

p_adjusted:

Integer, p_value adjusted

event_position:

Integer, the position middle between 2 fragments with an event

velocity_ratio:

Integer, ratio of velocity between 2 delay 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

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:

The bin/probe specific strand

TU:

The overarching transcription unit

segment_1:

String, the first fragment of the two of fragments subjected to analysis

segment_2:

String, the second fragment of the two of fragments subjected to analysis

event_duration:

Integer, the duration between two delay fragments

gap_fragments:

Integer, the distance between two delay fragments

features:

Integer, number of fragements involved on the event

events_velocity_df:

all information regarding events related to velocity:

event:

String, event type

p_value:

Integer, p_value of the event

p_adjusted:

Integer, p_value adjusted

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:

The bin/probe specific strand

TU:

The overarching transcription unit

segment_1:

String, the first fragment of the two of fragments subjected to analysis

segment_2:

String, the second fragment of the two of fragments subjected to analysis

event_duration:

Integer, the duration between two delay fragments

gap_fragments:

Integer, the distance between two delay fragments

features:

Integer, number of fragements involved on the event

TI_df:

all information regarding TI:

event:

String, event type

TI_fragment:

String, the fragment with TI

TI_termination_factor:

String, the factor of TI fragment

p_value:

Integer, p_value of the event

p_adjusted:

Integer, p_value adjusted

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:

The bin/probe specific strand

TU:

The overarching transcription unit

features:

Integer, number of fragements involved on the event

event_position:

Integer, the position middle between 2 fragments with an event

position_1:

the first position of TI fragment, if 2 fragments, first position is from the first fragment

position_2:

the last position of TI fragment, if 2 fragments, last position is from the second fragment.

Source

https://github.com/CyanolabFreiburg/rifi

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