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Data_file_descriptions.txt
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Data_file_descriptions.txt
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## Description of data files for "The battle of the sexes in humans is highly polygenic"
The files can be found on Zenodo (https://doi.org/10.5281/zenodo.11992199).
######################
1. Simulation results
---
File: "ML_simulations_all_results.txt"
---
d: Distance factor, the position of the true target of selection in terms of LD (r) with site 0
true_s: The true value of the selection coefficient
p1: Frequency of allele 1 at site 1
px: True frequency of allele 1 at the center site (site x)
p0: Frequency of allele 1 at site 0
D_10: The linkage disequilibrium (D) between sites 1 and 0
r_10: The correlation (r) between sites 1 and 0
int_s: The optimized, maximum likelihood value for the selection coefficient for the haplotype method (interpolation)
int_ml: The log likelihood for the value of int_s
sing_s: The optimized, maximum likelihood value for the selection coefficient using single sites
sing_ml: The log likelihood for the value of sing_s
px_hat: The assumed value for frequency of allele 1 at the center site (site x)
---
File: "ML_simulations_all_bias.txt"
---
d: Distance factor, the position of the true target of selection in terms of LD (r) with site 0
true_s: The true value of the selection coefficient
Bias_int: Mean bias of int_s across all runs of a given d value
Bias_sing: Mean bias of sing_s across all runs of a given d value
abs_Bias_int: Absolute value of Bias_int
abs_Bias_sing: Absolute value of Bias_sing
RelErr_int: Mean relative error of int_s across all runs of a given d value
RelErr_sing: Mean relative error of sing_s across all runs of a given d value
abs_RelErr_int: Absolute value of RelErr_int
abs_RelErr_sing: Absolute value of RelErr_sing
---
File: "ML_simulations_all_MSE.txt"
---
d: Distance factor, the position of the true target of selection in terms of LD (r) with site 0
true_s: The true value of the selection coefficient
MSE_int: Mean-squared error for int_s across all runs of a given d value
MSE_sing: Mean-squared error for sing_s across all runs of a given d value
UpperCI_int: Upper value of the 95% confidence interval of the mean-squared error for int_s obtained from bootstrapping
LowerCI_int: Lower value of the 95% confidence interval of the mean-squared error for int_s obtained from bootstrapping
UpperCI_sing: Upper value of the 95% confidence interval of the mean-squared error for sing_s obtained from bootstrapping
LowerCI_sing: Lower value of the 95% confidence interval of the mean-squared error for sing_s obtained from bootstrapping
######################
2. UKB Results
---
File: "UKB_mafs_r2_genotyped.txt" (QC filtered, phased genotyped MAFs and pair-wise r2 values from PLINK)
---
Chrom: Chromosome
BP_A: Base-pair coordinate of variant A (first variant)
SNP_A: rsID of SNP A
MAF_A: Minor allele frequency at SNP A
BP_B: Base-pair coordinate of variant B (second variant)
SNP_B: rsID of SNP B
MAF_B: Minor allele frequency at SNP B
R2: Squared correlation coefficient between A and B
---
File: "UKB_mafs_imputed_filtered.txt" (QC filtered vector of MAFs from the UKB imputed dataset)
---
Vector of minor allele frequency values
---
File: "UKB_r2_genotyped_filtered.txt" (QC filtered vector of r2 values from phased SNPs)
---
Vector of r2 values
---
Files: "UKB_haplotype_counts_5-22.txt" (all haplotype counts, 2 site windows)
"UKB_haplotype_permcounts_5-22.txt" (all permuted haplotype counts, 2 site windows)
---
Chrom: Chromosome
Window: Window number on chromosome
haplotype: Haplotype designation in base 10 (0-3)
female_counts: number of given haplotype in females
male_counts: number of given haplotype in males
female_lrs: total number of recorded children in females with given haplotype
male_lrs: total number of recorded children in males with given haplotype
female_lrs2: total number of recorded children in females with given haplotype (halved)
male_lrs2: total number of recorded children in males with given haplotype (halved)
adj_female_counts: projected number of given haplotype in females (weighted by lrs)
adj_male_counts: projected number of given haplotype in males (weighted by lrs)
Leading_Position: Position of site 1 on chromosome
Leading_SNP: rsID of SNP at site 1
Leading_MAF: The minor allele frequency (MAF) given by UKB at site 1
Leading_Allele0: The genotype call for allele 0 at site 1
Leading_Allele1: The genotype call for allele 1 at site 1
---
File: "UKB_all_5-22.txt" (raw estimates)
---
Chrom: Chromosome
Window: Window number on chromosome
Site1_Position: Position of site 1 on chromosome
Site1_SNP: rsID of SNP at site 1
Site1_MAF: The minor allele frequency (MAF) given by UKB at site 1
Site1_Allele0: The genotype call for allele 0 at site 1
Site1_Allele1: The genotype call for allele 1 at site 1
Site0_Position: Position of site 0 on chromosome
Site0_SNP: rsID of SNP at site 0
Site0_MAF: The minor allele frequency (MAF) given by UKB at site 0
Site0_Allele0: The genotype call for allele 0 at site 0
Site0_Allele1: The genotype call for allele 1 at site 0
r_10: The correlation (r) between sites 1 and 0
r_1x: The estimated correlation (r) between site 1 and unknown site x
r_x0: The estimated correlation (r) between unknown site x and site 0
D_10: Linkage disequilibrium (in terms of D) between sites 1 and 0
D_1x: Estimated linkage disequilibrium (in terms of D) between site 1 and unknown site x
D_x0: Estimated linkage disequilibrium (in terms of D) between unknown site x and site 1
s_int_viability: Estimated viability selection coefficient at site "x" using haplotypes, likelihood
ML_int_viability: Log likelihood for s_int_viability
SE_v: Standard error for s_int_viability (from bootstrapping)
Z_v: Z-score for s_int_viability
Pval_int_boot_viability: P-value for s_int_viability (from SE_v)
s_site1_viability: Estimated viability selection coefficient at site 1, likelihood
ML_site1_viability: Log likelihood for s_site1_viability
s_site0_viability: Estimated viability selection coefficient at site 0, likelihood
ML_site0_viability: Log likelihood for s_site0_viability
s_int_fecundity: Estimated fecundity selection coefficient at site "x" using haplotypes, derived
SE_f: Standard error for s_int_fecundity (from bootstrapping)
Z_f: Z-score for s_int_fecundity
Pval_int_boot_fecundity: P-value for s_int_fecundity(from SE_f)
s_site1_fecundity: Estimated fecundity selection coefficient at site 1, derived
s_site0_fecundity: Estimated fecundity selection coefficient at site 0, derived
s_int_total: Estimated total selection coefficient at site "x" using haplotypes, likelihood
ML_int_total: Log likelihood for s_int_total
SE_t: Standard error for s_int_total (from bootstrapping)
Z_t: Z-score for s_int_total
Pval_int_boot_total: P-value for s_int_total (from SE_t)
s_site1_total: Estimated total selection coefficient at site 1, likelihood
ML_site1_total: Log likelihood for s_site1_total
s_site0_total: Estimated total selection coefficient at site 0, likelihood
ML_site0_total: Log likelihood for s_site0_total
r_10_perm: The correlation (r) between sites 1 and 0 (permuted)
r_1x_perm: The estimated correlation (r) between site 1 and unknown site x (permuted)
r_x0_perm: The estimated correlation (r) between unknown site x and site 0 (permuted)
D_10_perm: Linkage disequilibrium (in terms of D) between sites 1 and 0 (permuted)
D_1x_perm: Estimated linkage disequilibrium (in terms of D) between site 1 and unknown site x (permuted)
D_x0_perm: Estimated linkage disequilibrium (in terms of D) between unknown site x and site 1 (permuted)
s_v_perm: Estimated viability selection coefficient at site "x" using haplotypes, likelihood (permuted)
ML_s_v_perm: Log likelihood for s_v_perm (permuted)
SE_v_perm: Standard error for s_int_viability_perm (from bootstrapping) (permuted)
Z_v_perm: Z-score for s_v_perm (permuted)
s_v_pval_perm: P-value for s_int_viability_perm (from SE_v_perm) (permuted)
s_site1_viability_perm: Estimated viability selection coefficient at site 1, likelihood (permuted)
ML_site1_s_v_perm: Log likelihood for s_site1_viability_perm (permuted)
s_site0_viability_perm: Estimated viability selection coefficient at site 0, likelihood (permuted)
ML_site0_s_v_perm: Log likelihood for s_site0_viability_perm
s_f_perm: Estimated fecundity selection coefficient at site "x" using haplotypes, derived (permuted)
SE_f_perm: Standard error for s_f_perm (from bootstrapping) (permuted)
Z_f_perm: Z-score for s_f_perm (permuted)
s_f_pval_perm: P-value for s_f_perm (from SE_f_perm) (permuted)
s_site1_fecundity_perm: Estimated fecundity selection coefficient at site 1, derived (permuted)
s_site0_fecundity_perm: Estimated fecundity selection coefficient at site 0, derived (permuted)
s_t_perm: Estimated total selection coefficient at site "x" using haplotypes, likelihood (permuted)
ML_s_t_perm: Log likelihood for s_t_perm (permuted)
SE_t_perm: Standard error for s_t_perm (from bootstrapping) (permuted)
Z_t_perm: Z-score for s_t_perm (permuted)
s_t_pval_perm: P-value for s_t_perm (from SE_t_perm) (permuted)
s_site1_total_perm: Estimated total selection coefficient at site 1, likelihood (permuted)
ML_site1_s_t_perm: Log likelihood for s_site1_total_perm (permuted)
s_site0_total_perm: Estimated total selection coefficient at site 0, likelihood (permuted)
ML_site0_s_t_perm: Log likelihood for s_site0_total_perm (permuted)
---
Files: "UKB_filtered_5-22.txt" (filtered window estimates),
"UKB_filtered_pruned_5-22.txt" (filtered and LD pruned estimates)
---
Chrom: Chromosome
Window: Window number on chromosome
Site1_Position: Position of site 1 on chromosome
Site1_SNP: rsID of SNP at site 1
Site1_MAF: The minor allele frequency (MAF) given by UKB at site 1
Site1_Allele0: The genotype call for allele 0 at site 1
Site1_Allele1: The genotype call for allele 1 at site 1
Site0_Position: Position of site 0 on chromosome
Site0_SNP: rsID of SNP at site 0
Site0_MAF: The minor allele frequency (MAF) given by UKB at site 0
Site0_Allele0: The genotype call for allele 0 at site 0
Site0_Allele1: The genotype call for allele 1 at site 0
s_v: Estimated viability selection coefficient at site "x" using haplotypes, likelihood
ML_s_v: Log likelihood for s_v
s_v_pval: P-value for s_v (from SE_v)
SE_v: Standard error for s_v (from bootstrapping)
Z_v: Z-score for s_v
s_site1_viability: Estimated viability selection coefficient at site 1, likelihood
ML_site1_s_v: Log likelihood for s_site1_viability
s_site0_viability: Estimated viability selection coefficient at site 0, likelihood
ML_site0_s_v: Log likelihood for s_site0_viability
s_v_perm: Estimated viability selection coefficient at site "x" using haplotypes, likelihood (permuted)
ML_s_v_perm: Log likelihood for s_v_perm (permuted)
s_v_pval_perm: P-value for s_v_perm (from SE_v_perm) (permuted)
SE_v_perm: Standard error for s_v_perm (from bootstrapping) (permuted)
Z_v_perm: Z-score for s_v_perm (permuted)
s_site1_viability_perm: Estimated viability selection coefficient at site 1, likelihood (permuted)
ML_site1_s_v_perm: Log likelihood for s_site1_viability_perm (permuted)
s_site0_viability_perm: Estimated viability selection coefficient at site 0, likelihood (permuted)
ML_site0_s_v_perm: Log likelihood for s_site0_viability_perm (permuted)
s_f: Estimated fecundity selection coefficient at site "x" using haplotypes, likelihood
s_f_pval: P-value for s_f (from SE_f)
SE_f: Standard error for s_f (from bootstrapping)
Z_f: Z-score for s_f
s_site1_fecundity: Estimated fecundity selection coefficient at site 1, derived
s_site0_fecundity: Estimated fecundity selection coefficient at site 0, derived
s_f_perm: Estimated fecundity selection coefficient at site "x" using haplotypes, likelihood (permuted)
s_f_pval_perm: P-value for s_f_perm (from SE_f_perm) (permuted)
SE_f_perm: Standard error for s_f_perm (from bootstrapping) (permuted)
Z_f_perm: Z-score for s_f_perm (permuted)
s_site1_fecundity_perm: Estimated fecundity selection coefficient at site 1, derived (permuted)
s_site0_fecundity_perm: Estimated fecundity selection coefficient at site 0, derived (permuted)
s_t: Estimated total selection coefficient at site "x" using haplotypes, likelihood
ML_s_t: Log likelihood for s_t
s_t_pval: P-value for s_t (from SE_t)
SE_t: Standard error for s_t (from bootstrapping)
Z_t: Z-score for s_t
s_site1_total: Estimated total selection coefficient at site 1, likelihood
ML_site1_s_t: Log likelihood for s_site1_total
s_site0_total: Estimated total selection coefficient at site 0, likelihood
ML_site0_s_t: Log likelihood for s_site0_total
s_t_perm: Estimated total selection coefficient at site "x" using haplotypes, likelihood (permuted)
ML_s_t_perm: Log likelihood for s_t_perm (permuted)
s_t_pval_perm: P-value for s_t_perm (from SE_t_perm) (permuted)
SE_t_perm: Standard error for s_t_perm (from bootstrapping) (permuted)
Z_v_perm: Z-score for s_t_perm (permuted)
s_site1_total_perm: Estimated total selection coefficient at site 1, likelihood (permuted)
ML_site1_s_t_perm: Log likelihood for s_site1_total_perm (permuted)
s_site0_total_perm: Estimated total selection coefficient at site 0, likelihood (permuted)
ML_site0_s_t_perm: Log likelihood for s_site0_total_perm (permuted)
---
File: "UKB_persite_estimates_5-20.txt" (single site estimates)
---
Chrom: Chromosome
Position: Position of SNP on chromosome
SNP: rsID of SNP at given position
MAF: Minor allele frequency at site
sv: Estimated viability selection coefficient at site
sv_perm: Estimated viability selection coefficient at site (permuted)
sf: Estimated fecundity selection coefficient at site
sf_perm: Estimated fecundity selection coefficient at site (permuted)
st: Estimated total selection coefficient at site
st_perm: Estimated total selection coefficient at site (permuted)
sf_F: Estimated fecundity selection coefficient at site in females
sf_M: Estimated fecundity selection coefficient at site in males
sf_F_perm: Estimated fecundity selection coefficient at site in females (permuted)
sf_M_perm: Estimated fecundity selection coefficient at site in males (permuted)
sf_prod: The product of sf_F and sf_M
sf_prod_perm: The product of sf_F_perm and sf_M_perm (permuted)
######################
5. Ensemble VEP output
---
Files: "UKB_VEP_viability_sighits_5-20.tsv"
"UKB_VEP_total_sighits_5-20.tsv"
---
See https://useast.ensembl.org/info/docs/tools/vep/vep_formats.html#output
######################
4. Summary GWAS and mash estimates for regressions, results
---
Files: "*.gwas_mash_summary.txt"
---
Chrom: Chromosome
Position: Position of SNP on chromosome
SNP: rsID of SNP at given position (lowest lfsr in window)
SNP_allele_0: Genotype call for allele 0
SNP_allele_1: Genotype call for allele 1
s_v: Estimated viability selection coefficient at site "x" using haplotypes, likelihood
SE_v: Standard error for s_v (from bootstrapping)
s_f: Estimated fecundity selection coefficient at site "x" using haplotypes, derived
SE_f: Standard error for s_f (from bootstrapping)
s_t: Estimated total selection coefficient at site "x" using haplotypes, likelihood
SE_t: Standard error for s_t (from bootstrapping)
Male_pm: mash-reduced effect size for trait in males estimated in Zhu et al (2023)
Male_psd: Standard deviation for Male_pm
Male_lfsr: Local false sign rate for Male_pm
Female_pm: mash-reduced effect size for trait in females estimated in Zhu et al (2023)
Female_psd: Standard deviation for Female_pm
Female_lfsr: Local false sign rate for Female_pm
A_male: Genotype call for allele 1 in males
A_female: Genotype call for allele 1 in females
block: Haplotype block number site is located in (coordinates from Berisa and Pickrell, 2016)
Effect_Diff: Difference in effect size (Male_pm-Female_pm)
varEffect: Variance of Effect_Diff
sdEffect: Standard deviation of Effect_Diff
---
File: "regression.lfsr.mash.p1.txt" (results from SMA regressions)
---
Trait: Phenotype name
Mode: Viability, Fecundity, or Total selection
Data: How SNPs were selected (random or by lowest LFSR)
mean_slope: Mean value of the slope from 1000 SMA regressions
SD_slope: Standard deviation of the SMA slope from 1000 regressions
Z: Z-score for the SMA regressions
sample_size_regression: Number of SNPs used in regression
SNPs_after_pval_filtering: Number of SNPs avaliable for sampling for trait
######################
5. ABC analysis
---
File: "FinalABC_50kSims.txt" (ABC results across 50k runs)
---
Column1: Priors for selection coefficient (s)
Column2: Priors for frequency of selection (F)
Column3: Sum of Squared Errors (SSE)
---
File: "ABC_Results_Top1Perc.txt" (accepted values at 1%)
---
accepted_s: Posterior values for the selection coefficient (s)
accepted_F: Posterior values for the frequency of selection (F)
---
File: "DownSampling_vs_ABCestimates.txt" (downsampling)
---
S_posterior_mode: Mode of the posterior values for the selection coefficient (s)
F_posterior_mode: Mode of the posterior values for the frequency of selection (F)
S_posterior_mean: Mean of the posterior values for the selection coefficient (s)
F_posterior_mean: Mean of the posterior values for the frequency of selection (F)
DownsamplePercent: Percentage of original runs (50k)
---
File: "Threshold_vs_ABCestimates.txt" (Varying acceptance thresholds)
---
S_posterior_mode: Mode of the posterior values for the selection coefficient (s)
F_posterior_mode: Mode of the posterior values for the frequency of selection (F)
S_posterior_mean: Mean of the posterior values for the selection coefficient (s)
F_posterior_mean: Mean of the posterior values for the frequency of selection (F)
Acceptance_Threshold: Acceptance threshold in ABC