filterTSS: Filter raw TSS counts or normalized TSS

In Linlab-slu/TSSr: TSS sequencing data analysis

Filter raw TSS counts or normalized TSS

Description

Filters transcriptional or sequencing noise.

Usage

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.

Value

Large List of elements - one element for each sample

Examples

data(exampleTSSr)
filterTSS(exampleTSSr, method = "TPM", tpmLow=0.1)

Linlab-slu/TSSr documentation built on Oct. 23, 2024, 8:31 p.m.