unlogtpm: Convert TPM to logTPM

In jlaffy/scalop: Single Cell Analysis Operations

Convert TPM to logTPM

Description

Convert TPM to logTPM, i.e. using log2(TPM/10 + 1).

Convert logTPM to TPM, i.e. using 10*(2^(TPM)-1).

Usage

logtpm(m, bulk = F)

unlogtpm(m, bulk = F)

Arguments

m	matrix of logTPM values (gene rows; cell columns)
bulk	if bulk then instead uses 2^(TPM)-1. i.e. no scaling. Default: F

Details

TPM/10 is used for single cells since 100,000 is a more reasonable estimate than 1,000,000 for the number of RNA transcripts in a cell. 1,000,000 is reasonable estimate for bulk samples that contain multiple cells.

TPM/10 is used for single cells since 100,000 is a more reasonable estimate than 1,000,000 for the number of RNA transcripts in a cell. 1,000,000 is reasonable estimate for bulk samples that contain multiple cells.

Value

TPM matrix

TPM matrix

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.