higbee_uploads

higbee_uploads.r

# on bc3

# wget https://fluff.bris.ac.uk/fluff/u2/mk19726/Al7MuuePNzS7tMWliJGG6QznF/fev1_adjusted_only_for_sex_imputed.txt
# wget https://fluff.bris.ac.uk/fluff/u2/mk19726/0ar7Sekl4I3Xj4JyatEf_wznc/fvc_adjusted_only_for_sex_imputed.txt
# wget https://fluff.bris.ac.uk/fluff/u4/mk19726/pUNC547Sala4I5Y1V_G9Bwzna/obstructive_ratio_spirometry_imputed.txt



# FEV1:
# sample size 353315
# http://www.ebi.ac.uk/efo/EFO_0004314 
# continuous trait. 
# "FEV1, best measure, adjusted for sex"
# 100% European
# Males and Females

# FVC:
# sample size 353315
# http://www.ebi.ac.uk/efo/EFO_0004312
# continuous trait
# "FVC, best measure, adjusted for sex"
# 100% European
# Males and Females

# FEV1/FVC <0.7:
# sample size 353315
# http://purl.obolibrary.org/obo/HP_0006536
# cases 55907, controls 297408
# "FEV1/FVC <0.7, adjusted for sex"
# 100% European
# Males and Females




library(GwasDataImport)
ieugwasr::get_access_token()


x1 <- Dataset$new(filename="fev1_adjusted_only_for_sex_imputed.txt")
x1$collect_metadata(list(
	trait="FEV1",
	author="Higbee D",
	year=2021,
	build="HG19/GRCh37",
	category="Risk factor",
	subcategory="NA",
	group_name="public",
	population="European",
	sex="Males and Females",
	note="UK Biobank IEU pipeline. FEV1 best measure, adjusted for sex",
	ontology="EFO:0004314",
	sample_size=353315,
	unit="litres",
	sd=0.78))

x1$determine_columns(list(snp_col="SNP", oa_col="ALLELE0", ea_col="ALLELE1", beta_col="BETA", se_col="SE", pval_col="P_BOLT_LMM_INF", chr_col="CHR", pos_col="BP", eaf_col="A1FREQ"))
x1$format_dataset()
x1$api_metadata_upload()
x1$api_gwasdata_upload()



x2 <- Dataset$new(filename="fvc_adjusted_only_for_sex_imputed.txt")
x2$collect_metadata(list(
	trait="FVC",
	author="Higbee D",
	year=2021,
	build="HG19/GRCh37",
	category="Risk factor",
	subcategory="NA",
	group_name="public",
	population="European",
	sex="Males and Females",
	note="UK Biobank IEU pipeline. FVC best measure, adjusted for sex",
	ontology="EFO:0004314",
	sample_size=353315,
	unit="litres",
	sd=0.984))

x2$determine_columns(list(snp_col="SNP", oa_col="ALLELE0", ea_col="ALLELE1", beta_col="BETA", se_col="SE", pval_col="P_BOLT_LMM_INF", chr_col="CHR", pos_col="BP", eaf_col="A1FREQ"))
x2$format_dataset()
x2$api_metadata_upload()
x2$api_gwasdata_upload()



x3 <- Dataset$new(filename="obstructive_ratio_spirometry_imputed.txt")
x3$collect_metadata(list(
	trait="FEV1/FVC < 0.7",
	author="Higbee D",
	year=2021,
	build="HG19/GRCh37",
	category="Risk factor",
	subcategory="NA",
	group_name="public",
	population="European",
	sex="Males and Females",
	note="UK Biobank IEU pipeline. FEV1/FVC < 0.7, adjusted for sex",
	ontology="HP:0006536",
	sample_size=353315,
	ncase = 55907,
	ncontrol = 297408,
	unit="risk difference"))

x3$determine_columns(list(snp_col="SNP", oa_col="ALLELE0", ea_col="ALLELE1", beta_col="BETA", se_col="SE", pval_col="P_BOLT_LMM_INF", chr_col="CHR", pos_col="BP", eaf_col="A1FREQ"))

x3$format_dataset()
x3$api_metadata_upload()
x3$api_gwasdata_upload()