apply_ancova: =========================================================================...

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

========================================================================= apply_ancova

apply_ancova checks the variances between 2 segments showing either pausing site (ps) or internal starting site (ITSS) independently.

Description

apply_ancova is a statistical test to check if fragments showing ps and ITSS events have significant slope using Ancova test.The function uses ancova test. Ancova is applied when the data contains independent variables, dependent variables and covariant variables. In this case, segments are independent variables, position is the dependent variable and the delay is the covariant.

Usage

apply_ancova(inp)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.

Value

the SummarizedExperiment with the columns regarding statistics:

ID:	The bin/probe specific ID.
position:	The bin/probe specific position.
strand:	The bin/probe specific strand.
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_duration:	Integer, the duration between two delay fragments.
event_ps_itss_p_value_Ttest:	p_value of pausing site or iTSS_I.
p_value_slope:	Integer, the p_value added to the inp
delay_frg_slope:	Integer, the slope value of the fit through the respective delay fragment
velocity_ratio:	Integer, the ratio value of velocity from 2 delay fragments

Examples

data(stats_minimal)
apply_ancova(inp = stats_minimal)

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