estimate_t: Find the most commonly occuring relative expression value in...

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Converting relative expression values to mRNA copies per cell requires knowing the most commonly occuring relative expression value in each cell This value typically corresponds to an RPC value of 1. This function finds the most commonly occuring (log-transformed) relative expression value for each column in the provided expression matrix.

Usage

estimate_t(relative_expr_matrix, relative_expr_thresh = 0.1)

Arguments

relative_expr_matrix	a matrix of relative expression values for values with each row and column representing genes/isoforms and cells, respectively. Row and column names should be included. Expression values should not be log-transformed.
relative_expr_thresh	Relative expression values below this threshold are considered zero.

Details

This function estimates the most abundant relative expression value (t^*) using a gaussian kernel density function. It can also optionally output the t^* based on a two gaussian mixture model based on the smsn.mixture from mixsmsn package

Value

an vector of most abundant relative_expr value corresponding to the RPC 1.

Examples

## Not run: 
HSMM_fpkm_matrix <- exprs(HSMM)
t_estimate = estimate_t(HSMM_fpkm_matrix)

## End(Not run)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.