res_example: Differential expression example for HCC vs adjacent liver...

In Bin-Chen-Lab/octad: Open Cancer TherApeutic Discovery (OCTAD)

Differential expression example for HCC vs adjacent liver tissue computed in diffExp() function

Description

Differential expression example for HCC vs adjacent liver tissue computed in diffExp() function

Usage

res_example

Format

A data.frame with 963 rows and 18 variables:

identifier

Ensg ID

log2FoldChange

Log2 fold-change

logCPM

log CPM value

LR

LR value

pvalue

p.value

padj

FDR

tax_id

taxon id

GeneID

Gene id

LocusTag

Locus tag

chromosome

Chromosome

map_location

Chromosome location

description

Full gene name

type

type of gene

Symbol_autho

HGNC symbol

other

Gene function

Details

To generate this dataset use the following code from the octad package #load data.frame with samples included in the OCTAD database.
phenoDF=.eh[['EH7274']]
#select data
HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'primary')
#select cases
case_id=HCC_primary$sample.id
control_id=subset(phenoDF,biopsy.site=='LIVER'&sample.type=='normal')$sample.id[1:50]
res=diffExp(case_id,control_id,source='octad.small',output=FALSE)

Bin-Chen-Lab/octad documentation built on Jan. 28, 2023, 11:20 p.m.