shiftedZScoreTx: Calculate shifted z scores over transcripts

In yue-wang-biomath/RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

Calculate shifted z scores over transcripts

Description

Calculate shifted z scores for permutation test results. It provides mode of shifting regions of interest over mRNA space.

Usage

shiftedZScoreTx(permTestTx_results = NULL, txdb = NULL, type = "normal",
window = 200, step = 20, ev_function_1 = overlapCountsTx, ...)

Arguments

permTestTx_results	A permTestTx.results object.
txdb	A TxDb object.
type	If type is "mature", regions of interest will be shifted over the mature mRNA space according to the input txdb object. Otherwise ROS will be shifted over genomic space.
window	The window of the whole shifting.
step	The step of each shifting.
ev_function_1	Evaluation function. Default is overlapCountsTx.
...	Any additional parameters needed.

Details

see examples in plotShiftedZScoreTx

Value

A list object, which is defined to be shiftedZScoreTx.results class. It contains the following items:

• shifted.z.scores: Standard z-scores after shifting.

• window: Window of the whole shifting.

• step: Step of each shifting.

• original.z.score: Original standard score.

See Also

plotShiftedZScoreTx

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
file <- system.file(package="RgnTX", "extdata", "m6A_sites_data.rds")
m6A_sites_data <- readRDS(file)
RS1 <- m6A_sites_data[1:100]
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
permTestTx_results <- permTestTxIA_customPick(RS1 = RS1,
                                              txdb = txdb,
                                              type = "mature",
                                              customPick_function = getStopCodon,
                                              ntimes = 1)
shiftedZScoreTx_results <- shiftedZScoreTx(permTestTx_results,txdb,
                                           type = 'mature',
                                           window = 500,
                                           step = 50,
                                           ev_function_1 = overlapCountsTxIA)

yue-wang-biomath/RgnTX documentation built on Aug. 24, 2023, 1:12 p.m.