filterTSS: Filter raw TSS counts or normalized TSS

Description Usage Arguments Examples

Description

Filters transcriptional or sequencing noise.

Usage

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filterTSS(object, method = "poisson", normalization = TRUE,
pVal =0.01, tpmLow = 0.1)

## S4 method for signature 'TSSr'
filterTSS(
  object,
  method = "poisson",
  normalization = TRUE,
  pVal = 0.01,
  tpmLow = 0.1
)

Arguments

object

A TSSr object.

method

Method to be used for TSS filtering: "poisson" or "TPM". "poisson" can be used only if the input TSS data in raw number of counts.

normalization

Define whether normalization data to TPM. Used only if method = “poisson”. Default is TRUE.

pVal

Used only if method = "poisson". Default value is 0.01.

tpmLow

Used only if method = "TPM". Default value is 0.1.

Examples

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filterTSS(exampleTSSr, method = "TPM", tpmLow=0.1)
filterTSS(exampleTSSr, method = "poisson", pVal = 0.01)

Linlab-slu/TSSr documentation built on July 28, 2021, 12:59 a.m.