Feature Weight Pro (FWP)

Feature-weight based measurement of cancerous transcriptome using cohort-wide and sample-specific information, Cellular Oncology, 2023, https://doi.org/10.1007/s13402-023-00879-6

Content:

• Usage
• Benchmark Dataset

Usage:

# R version 4.2.0

library('data.table') # 1.14.6
library('irlba') # 2.3.5.1
library('pROC') # 1.18.2

source('fwp.R')

TRAIN.TYPE='PCPG'
TEST.TYPE='PCPG'

TRAIN.DATA=.loadFileNoGap(paste0('./data/first/',TRAIN.TYPE,'/mat_train.tsv'))
TRAIN.TAG=read.csv(paste0('./data/first/',TRAIN.TYPE,'/CorrectDP_train.csv'),header=F)
TEST.DATA=.loadFileNoGap(paste0('./data/first/',TEST.TYPE,'/mat_test.tsv'))
TEST.TAG=read.csv(paste0('./data/first/',TEST.TYPE,'/CorrectDP_test.csv'),header=F)

# DATA: a matrix (Row: genes; Column: samples); after normalization (e.g. fpkm)
# TAG: a vector (Tumor: 1; Normal: 0)

# step1. calculate feature-weight (FW)
FW=.calFW(TRAIN.DATA, TRAIN.TAG[,2])

# OR, you can directly load our pre-trained FW file. 
# https://github.com/jumphone/FWP/tree/main/feature_weight/TCGA_bulkRNA
FW=readRDS('FW_bulk_TCGA_PCPG.rds') 

# step2. calculate score
out.fwp=fwp(TEST.DATA, FW)

# step3. evaluation
result=.evaluate(out.fwp, TEST.TAG[,2])   
print(result)

Benchmark Dataset:

Pre-trained Feature-Weight Files:

RDS files: https://github.com/jumphone/FWP/tree/main/feature_weight/TCGA_bulkRNA

Processed Data:

Baidu Cloud Storage：https://pan.baidu.com/s/1WxImyznSwDtlox7bh0EyGg?pwd=ilj2

In the processed data, "correctDP" stands for "correct data phenotype".

In the "Baidu Cloud Storage", we provide the processed data of bulk & single-cell RNA-seq data.

The processed spatial data is too large to upload.

Raw Data:

bulk RNA-seq (UCSC Xena): https://xenabrowser.net/datapages/

single-cell & spatial RNA-seq, Wu et al., Nat Genet, 2021: GSE176078 (GEO database)

single-cell RNA-seq, oligodendroglioma: GSE70630

spatial RNA-seq, pancreatic ductal adenocarcinoma (PDAC): GSE211895 (raw counts); https://github.com/anvaly/SpatialPortal (metadata)

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More tools & studies: https://fzhang.bioinfo-lab.com/