gridSearch: gridSearch perform grid searching for the best parameter...

In zhushijia/STAR2bSMRT: STARlong and STARshort based Single Molecule Real Time Iso-Seq analysis

Description

gridSearch perform grid searching for the best parameter settings for thresSR and thresDis, by maximizing the correlation between long and short read junction sites

Usage

gridSearch(LRjunc, SRjunc, thresSR = c(1:30), thresDis = c(1:20),
  adjustNCjunc = TRUE, matchedLS = NULL, fuzzyMatch = 100)

Arguments

LRjunc	a list of data frame, indicating the splicing junction sites obtained from long reads
SRjunc	a list of data frame, indicating the splicing junction sites obtained from short reads
thresSR	a vector of integers indicating the searching range for the number of short reads which support the splicing junction sites.
thresDis	a vector of integers indicating the searching range for the tolerance distance between short read-derived splicing junction and long read-derived junction. STAR2bSMRT will correct the long read-derived junction to the short read-derived junction, if more short reads than defined thresSR support that short read-derived junction, and the distance between long and short read junctions is shorter than the defined thresDis.
adjustNCjunc	boolean value indicating whether to minimize the non-canonical junction sites.
matchedLS
fuzzyMatch	integer value indicating the distance for fuzzyMatch

Value

a matrix of correlation coefficients between long and short read junctions, with the row representing the number of short reads, the column representing the distance between long and short junctions

zhushijia/STAR2bSMRT documentation built on Dec. 18, 2019, 7:37 a.m.