permTestTxIA: Perform permutation test

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

Perform permutation test

Description

Perform permutation test for evaluating spatial association between some features (with isoform ambiguity) and a region set. It randomizes the features and compares it with the region set to see if there is an association between the features and the region set. The difference between this function and permTestTx is that it is for RNA-related genomic features that have isoform ambiguity, i.e., features that one does not know which transcript they comes from.

Usage

permTestTxIA(RS1 = NULL,
                    RS2 = NULL,
                    txdb = NULL,
                    type = 'mature',
                    ntimes = 50,
                    ev_function_1 = overlapCountsTx,
                    ev_function_2 = overlapCountsTx,
                    pval_z = FALSE,
                    ...)

Arguments

RS1	The feature set to be randomized. It should be in the GRanges or GRangesList format.
RS2	The region set to be compared with. It should be in the GRanges or GRangesList format.
txdb	A TxDb object.
type	A character object. Default is "mature". It accepts options "mature", "full", "fiveUTR", "CDS" or "threeUTR", with which one can get corresponding types of transcriptome regions.
ntimes	Randomization times.
ev_function_1	Evaluation function defines what statistic to be tested between RS1 and RS2. Default is overlapCountsTx.
ev_function_2	Evaluation function defines what statistic to be tested between each element in RSL and RS2. Default is overlapCountsTx.
pval_z	Boolean. Default is FALSE. If FALSE, the p-value is calculated based on the number of random evaluations is larger or less than the initial evaluation. If TRUE, the p-value is calculated based on a z-test.
...	Any additional parameters needed.

Details

permTestTxIA only needs users to input two region sets. It will automatically randomize the first region set into transcriptome.

Value

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

• RSL: Randomized region sets of RS1.

• RS1: The feature set to be randomized.

• RS2: The region set to be compared with the feature set.

• orig.ev: The value of overlapping counts between RS1 and RS2.

• rand.ev: The values of overlapping counts between each element in RSL and RS2.

• pval: p-value of the test.

• zscore: Standard score of the test.

See Also

plotPermResults

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[1:500]
trans.ids <- getTransInfo(RS1, txdb)[, "trans_ID"]
RS2 <- getStopCodon(trans.ids, txdb)

permTestTx_results <- permTestTxIA(RS1 = RS1, RS2 = RS2,
                            txdb = txdb, ntimes = 5)

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