
prs <- read.table("/dartfs-hpc/rc/home/m/f0052zm/szhao_lab_share/diffDriver/data_run_prs/pancancer_20211020/pheno_combine.txt", header = T)


nrow(prs)


info <- read.csv("/dartfs-hpc/rc/home/m/f0052zm/szhao_lab_share/jihyun/PRSs_TCGA/Traits.csv")


info


prscor <- cor(prs[, 4:ncol(prs)])


options(repr.plot.width = 8, repr.plot.height = 6)
library(pheatmap)
pheatmap(prscor, fontsize_row = 8, fontsize_col=6, angle_col = 45, treeheight_row = 50, treeheight_col =0)

ï..Trait	Abbr.	Sample.Size	Data.Source	PRSs.File
Intelligence	IQ	269,867	Savage et al. Nat Genet 2018	TCGA_HM3_IQ_NG_2018.profile
Rheumatoid arthritis	RA	41,282	Stahl et al. Nat Genet 2010	TCGA_HM3_RA_NG2010.hap3.profile
Smoking cessation	SC	547,219	Liu et al. Nat Genet 2019	TCGA_HM3_SmokingCessation.profile
Education attainment	EA	766,345	Lee et al. Nat Genet 2018	TCGA_HM3_EA_NG_2018_excluding_23andMe.profile
Vitiligo	VIG	44,266	Jin et al. Nat Genet 2016	TCGA_HM3_Vitiligo.profile
Smoking initiation	SI	1,232,091	Liu et al. Nat Genet 2019	TCGA_HM3_SmokingInitiation.profile
Major depressive disorder	MDD	101,498	Wray et al. Nat Genet 2018	TCGA_HM3_MDD_NG_2018.profile
Alcohol consumption	AC	941,280	Liu et al. Nat Genet 2019	TCGA_HM3_DrinksPerWeek.profile
Ulcerative Colitis	UC	27,432	Liu et al. Nat Genet 2015	TCGA_HM3_UC_NG_2015.profile
Subjective well-being	SWB	298,420	Okbay et al. Nat Genet 2015	TCGA_HM3_SWB_NG_2015.profile
Total body bone mineral density	BMD	66,628	Medina Gomez et al. AJHG 2018	TCGA_HM3_BMD_2018.profile
Stroke	Stroke	446,696	Malik et al. Nat Genet 2018	TCGA_HM3_Stroke_GWAS_2018.profile
Type 2 diabetes	T2D	158,186	Scott et al. Nat Genet 2017	TCGA_HM3_T2D_DIAGRAM_2017.profile
Bipolar disorder	BIP	41,653	BDSWGPGC Cell 2018	TCGA_HM3_BIP_Cell_2018.profile
Schizophrenia	SCZ	65,967	BDSWGPGC Cell 2018	TCGA_HM3_SCZ_Cell_2018.profile
Parkinson's disease	PD	308,518	Chang et al. Nat Genet 2017	TCGA_HM3_PD_GWAS_2017_N300k.profile
Inflammatory bowel disease	IBD	34,652	De Lange et al. Nat Genet 2017	TCGA_HM3_IBD_NG2017.hap3.profile
Breast cancer	BR	228,951	Michailidou et al. Nature 2018	TCGA_HM3_Breast_Cancer.profile
Cigarette per day	CPD	262,014	Liu et al. Nat Genet 2019	TCGA_HM3_CigarettesPerDay.profile
Allergic disease	AD	59,832	Ferreira et al. Nat Genet 2017	TCGA_HM3_Allergic_disease.profile
Ovarian cancer	OV	66,450	Kuchenbaecker et al. Nat Genet 2015	TCGA_HM3_Ovarian_cancer.profile
Prostate cancer	PR	140,254	Schumacher et al. Nat Genet 2017	TCGA_HM3_Prostate_cancer_2017_common.profile
Asthma	ASM	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_ASTHMA.profile
Height	Height	344,664	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_Height.profile
Disease status	CASE	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_CASES.profile
Obesity	OBES	258,442	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_OBESITY.profile
Iron deficiency anemias	ID	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_IRON_DEFICIENCY.profile
Cancer	CA	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_CANCER.profile
Varicose veins of lower extremities	VV	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_VARICOSE_VEINS.profile
Body mass index	BMI	344,306	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_BMI.profile
Osteoarthritis	OSTA	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_OSTIOA.profile
Hypertensive disease	HYPE	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_HYPER.profile
Coffee intake	CI	421,947	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_CI_cojo.profile
Type 2 diabetes	DIA2	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_DIA2.profile
Irritable bowel syndrome	IBS	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_IRRITABLE_BOWEL.profile
Hernia abdominopelvic cavity	HA	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_HERNIA_ABDOMINOPELVIC.profile
Severe obesity	SO	157,142	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_SEVERE_OBESITY.profile
Cardiovascular disease	CARD	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_CARD.profile
Dyslipidemia	DY	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_DYSLIPID.profile
Tea intake	TI	440,094	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_TI_cojo.profile
Peptic ulcers	PU	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_PEPTIC_ULCERS.profile
Allergic rhinitis	AR	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_ALLERGIC_RHINITIS.profile
Psychiatric disorder	PSYD	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_PSYCHIATRIC.profile
Peripheral vascular disease	PVD	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_PVD.profile
Osteoporosis	OSTP	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_OSTIOP.profile
Hemorrhoids	HEMO	452,272	Zeng et al. bioRxiv 2019	TCGA_HM3_ukbEUR_HEMORRHOIDS.profile

PRS score¶