ewce_expression_data: Bootstrap celltype enrichment test for transcriptome data

Description Usage Arguments Value Examples

View source: R/ewce_expression_data.r

Description

ewce_expression_data takes a differential expression table and determines the probability of cell-type enrichment in the up & down regulated genes

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
ewce_expression_data(
  sct_data,
  annotLevel = 1,
  tt,
  sortBy = "t",
  thresh = 250,
  reps = 100,
  ttSpecies = "mouse",
  sctSpecies = "mouse"
)

Arguments

sct_data

List generated using generate_celltype_data

annotLevel

an integer indicating which level of the annotation to analyse. Default = 1.

tt

Differential expression table. Can be output of limma::topTable function. Minimum requirement is that one column stores a metric of increased/decreased expression (i.e. log fold change, t-statistic for differential expression etc) and another contains either HGNC or MGI symbols.

sortBy

Column name of metric in tt which should be used to sort up- from down- regulated genes. Default="t"

thresh

The number of up- and down- regulated genes to be included in each analysis. Default=250

reps

Number of random gene lists to generate (default=100 but should be over 10000 for publication quality results)

ttSpecies

Either 'mouse' or 'human' depending on which species the differential expression table was generated from

sctSpecies

Either 'mouse' or 'human' depending on which species the single cell data was generated from

Value

A list containing five data frames:

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
library(ewceData)
# Load the single cell data
ctd <- ctd()

# Set the parameters for the analysis
# Use 3 bootstrap lists for speed, for publishable analysis use >10000
reps <- 3
# Use 5 up/down regulated genes (thresh) for speed, default is 250
thresh = 5
annotLevel <- 1 # <- Use cell level annotations (i.e. Interneurons)

# Load the top table
tt_alzh <- tt_alzh()

tt_results <- ewce_expression_data(
    sct_data = ctd, tt = tt_alzh, annotLevel = 1, thresh = thresh,
    reps = reps, ttSpecies = "human", sctSpecies = "mouse"
)

NathanSkene/EWCE documentation built on June 19, 2021, 5:40 a.m.