dataframe_summary: =========================================================================...

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

========================================================================= dataframe_summary

dataframe_summary creates two tables relating gene annotation to fragments

Description

dataframe_summary creates two tables summary of segments and their half-lives. The first output is bin/probe features and the second one is intensity fragment based.The dataframe_summary creates one table with feature_type, gene, locus_tag, position, strand, TU, delay_fragment, HL_fragment, half_life, intensity_fragment, intensity and velocity. The second table is similar to the first one but in compact form. It contains the same columns, the only difference is on position where a start and end position are indicated separately.

Usage

dataframe_summary(data, input)

Arguments

data	SummarizedExperiment: the input data frame with correct format.
input	dataframe: dataframe from event_dataframe function.

Value

bin_df:

all information regarding bins: position: Integer, position of the bin/probe on the genome 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 (+/-) segment: String, the bin/probe segment on the genome TU: String, The overarching transcription unit delay_fragment: The delay fragment the bin belongs to delay: Integer, the delay value of the bin/probe HL_fragment: The half-life fragment the bin belongs to half_life: The half-life of the bin/probe intensity_fragment: The intensity fragment the bin belongs to intensity: The relative intensity at time point 0 flag: String, the flag of the bin/probe, contains information or the distribution for the #'different fitting models TI_termination_factor: String, the TI termination factor determined by TI

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: Integer, the bin/probe specific first position last_position_frg: Integer, the bin/probe specific last position strand: Boolean. The bin/probe specific strand (+/-) TU: String, The overarching transcription unit segment: String, the bin/probe segment on the genome delay_fragment: String, the delay fragment the bin belongs to HL_fragment: Integer, the half_life fragment of the bin/probe belongs to half_life: Integer, the half-life of the bin/probe HL_SD: Integer, the half-life standard deviation of the HL fragment, bin/probe based HL_SE: Integer, the half-life standard error of the HL fragment, bin/probe based intensity_fragment: Integer, the intensity fragment the bin belongs to intensity: Integer, the relative intensity of bin/probe at time point 0 intensity_SD: Integer, the intensity standard deviation of the intensity fragment, bin/probe based intensity_SE: Integer, the intensity standard error of the intensity fragment, bin/probe based velocity: The velocity value of the respective delay fragment

Examples

data(stats_minimal)
data(res_minimal)
dataframe_summary(data = stats_minimal, input = res_minimal)

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