getRegions {dStruct} | R Documentation |
This function takes between- and within-group d scores for a transcript as input and identifies regions where the former is generally larger. Regions that pass minimum quality and minimum signal criteria are returned.
getRegions( d_within, d_spec, rdf, min_length = 11, check_signal_strength = TRUE, check_nucs = TRUE, check_quality = TRUE, quality = 0.5, evidence = 0, signal_strength = 0.1 )
d_within |
Nucleotide-wise d score for within-group variation. |
d_spec |
Nucleotide-wise d score for between-group variation. |
rdf |
Dataframe of reactivities for each sample. |
min_length |
Minimum length of constructed regions. |
check_signal_strength |
Logical, if TRUE, construction of regions must be based on nucleotides that have a minimum absolute value of reactivity. |
check_nucs |
Logical, if TRUE, constructed regions must have a minimum number of nucleotides participating in Wilcoxon signed rank test. |
check_quality |
Logical, if TRUE, check constructed regions for quality. |
quality |
Worst allowed quality for a region to be tested. |
evidence |
Minimum evidence of increase in variation from within-group comparisons to between-group comparisons for a region to be tested. |
signal_strength |
Threshold for minimum signal strength. |
Integer vector of nucleotides that constitute potential differentially reactive regions.
Krishna Choudhary
Choudhary, K., Lai, Y. H., Tran, E. J., & Aviran, S. (2019). dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome biology, 20(1), 1-26.