de_ttest: Run a DE between two groups with Welch's t-test

In marcalva/diem: Debris-Containing Droplet Identification using EM

Run a DE between two groups with Welch's t-test

Description

Run DE between two groups. x is a sparse matrix with count data. These counts can be normalized, or raw counts can be given. If providiing raw counts, set the normalize parameter to TRUE. c1 and c2 are vectors containing indices or names of the columns, or boolean indicies for the droplets A Welch's t-test is performed.

Usage

de_ttest(x, c1, c2, normalize = FALSE, sf = 1)

Arguments

x	A sparse matrix
c1	Column indexes or names of first group
c2	Column indexes or names of second group
normalize	Whether to scale the droplets to sum to sf and and then log transform.
sf	Scale the counts in each droplet to sum to this value.

Value

A data frame of DE results with

gene

gene name

diff

difference between mu1 and mu2

logFC

log2 fold change

mu1

mean of group 1

mu2

mean of group 2

t

t statistic

p

p-value

marcalva/diem documentation built on Jan. 1, 2023, 2:33 a.m.