GiGList.Analysis: Summary generator for a G4-iM Grinder resulting list...

In EfresBR/G4iMGrinder: G4iMGrinder: G4 Quadruplex, i-Motif and higher-order structures in DNA and RNA sequences search and analysis tool.

Description

To summarize the results of a GiGList into a single row. Allows easier comparison between genomes.

Usage

GiGList.Analysis(GiGList, iden, ScoreMin = c(20, 40), FreqMin = 10, LengthMin = 50, Density = 100000, byDensity = TRUE)

Arguments

GiGList	List, G4iMGrinder results in the form of a GiGList to analyse.
iden	character, identification tag of the DNA or RNA origin.
ScoreMin	integer or vector of integers, score filter to apply to the results. The function will create a new column for each integer in the vector with the filtrate results that score at least the value. Values are interpreted as absolute; if the search involves i-Motif detection, it will multiply by -1 to adapt to its scoring scale. The factory-fresh default is c(20, 40), returning the values of sequences that have at least high probability of formation (Scoremin >= 40 for PQS; Scoremin <= -40 for PiMS), and at least medium probability of formation (Scoremin >= 20 for PQS; Scoremin <= -20 for PiMS).
FreqMin	integer or vector of integers, frequency filter to apply to the results. The function will create a new column for each integer in the vector with the filtrate results that have a frequency of appearence in the genome of at least the value/s. The factory-fresh default is 10, returning the results detected with Freqmin >= 10.
LengthMin	integer or vector of integers, length filter to apply to the results. The function will create a new column for each integer in the vector with the filtrate results that have a frequency of appearence in the genome of at least the value/s. Only for Method 3 results (M3a and M3b). The factory-fresh default is 50, returning the results detected with Lengthmin >= 50.
Density	integer, constant to calculate density results. The factory-fresh default is 100000, returning results found per 100000 nucleotides. Only pertinent if byDensity = TRUE.
byDensity	logical, should the results be returned as a density. Calculated as Result.Density = (Density*Results)/(total genomic length). If set to FALSE, it will return counts. Density allows genomic size-indepedent comparisons. The factory-fresh default is TRUE.

Value

The result of GiGList.Analysis is a one row data.frame with the summary of the G4-iM Grinder List.

Column Meanings

Name: name of summary, given by the name of the GiGList input.

iden: identification of the genome, given by iden input.

Length: Length of the genomic sequence.

SeqG: percentage of the genomic sequence which is G.

SeqC: percentage of the genomic sequence which is C.

nM2a (column name prefix): results for Method 2a results if method is active. Returned as counts or density.

nM2b (column name prefix): results for Method 2b results if method is active. Returned as counts or density.

nM3a (column name prefix): results for Method 3a results if method is active. Returned as counts or density.

nM3b (column name prefix): results for Method 3b results if method is active. Returned as counts or density.

.S|X| (column name suffix): results for method filtered by score criteria. Within bars, the criteria. Returned as counts or density.

.F|X| (column name suffix): results for method filtered by frequency criteria. Within bars, the criteria. Returned as counts or density.

.L|X| (column name suffix): results for method filtered by length criteria. Within bars, the criteria. Returned as counts or density.

.KTFQ (column name suffix): results for method which have known-to-form-quadruplex within. Returned as counts or density.

.KNTFQ (column name suffix): results for method which have known-NOT-to-form-quadruplex within. Returned as counts or density.

.UniqPercent (column name suffix): percentage of result uniqueness per method. Calculated as: 100*[Number results with frequency of 1]/[total number of results]

Config: column with analysis information of summary.

Warning

Column names depend on summary conditions and hence the same analysis conditions must be used in order to bind GiG.List analysis together. The analysis with different G4-iM Grinder conditions may also give rise to problems when binding results.

Author(s)

Efres Belmonte-Reche

Examples

  # Creating the G4iMGrinder Results for the DNA search of G-quadruplex.
  Rs <- G4iMGrinder(Name = Name, Sequence = Sequence)

  # Creating the summary data.table
  Summary <- GiGList.Analysis(GiGList = Rs, iden = "Parasite")

EfresBR/G4iMGrinder documentation built on June 11, 2021, 2:57 a.m.