File formats#

.sumstats#

GWAS summary statistics following the LDSC format.

Example .sumstats file#

GENE

BMI

HEIGHT

SNP

A1

A2

N

CHISQ

Z

rs7899632

A

G

59957

3.4299

-1.852

rs3750595

A

C

59957

3.3124

1.82

.h5ad#

Single-cell data .h5ad file as defined in AnnData and Scanpy.

pval_file,zscore_file#

GWAS gene-level p-values / z-scores for different traits. A .tsv file with first column corresponding to genes and other columns corresponding to p-values / z-scores of traits (one trait per column).

Example pval_file#

GENE

BMI

HEIGHT

OR4F5

0.001

0.01

DAZ3

0.01

0.001

.gs#

scDRS gene set file. A .tsv file with two columns ["TRAIT", "GENESET"] and one line per trait. Can be generated using customized code or from p-value or z-score files using scDRS CLI scdrs munge-gs.

TRAIT

Trait (gene set) identifier.

GENESET

Comma-separated list of gene-weight pairs with the form “gene1:weight1,gene2:weight2,…” or “gene1,gene2,…” (meaning weights are 1).

Example weighted .gs file#

TRAIT

GENESET

PASS_HbA1C

FN3KRP:1.2,FN3K:2.3,HK1:4.7,GCK:5.2

PASS_MedicationUse_Wu2019

FTO:3,SEC16B:0.6,ADCY3:1.5,DNAJC27:1.3
Example unweighted .gs file#

TRAIT

GENESET

PASS_HbA1C

FN3KRP,FN3K,HK1,GCK

PASS_MedicationUse_Wu2019

FTO,SEC16B,ADCY3,DNAJC27

.cov#

scDRS covariate file for the .h5ad single-cell data. .tsv file.

  • First column: cell names, consistent with adata.obs_names.

  • Other comlumns: covariates with numerical values.

Example .cov file#

index

const

n_genes

sex_male

age

A10_B000497_B009023_S10

1

2706

1

18

A10_B000497_B009023_S10

1

2501

0

24

<trait>.score.gz#

scDRS score file for a give trait. .tsv.gz file.

  • First column: cell names, should be the same as adata.obs_names.

  • raw_score: raw disease score.

  • norm_score: normalized disease score.

  • mc_pval: cell-level MC p-value. Raw p-value without multiple testing adjustment.

  • pval: cell-level scDRS p-value. Raw p-value without multiple testing adjustment.

  • nlog10_pval: -log10(pval).

  • zscore: z-score converted from pval.

Example <trait>.score.gz file#

index

raw_score

norm_score

mc_pval

pval

nlog10_pval

zscore

A10_B000497_B009023_S10

0.730

7.04

0.0476

0.00166

2.78

2.94

A10_B000756_B007446_S10

0.725

7.30

0.0476

0.00166

2.78

2.94

<trait>.full_score.gz#

scDRS full score file for a give trait. .tsv.gz file.

  • All columns of {trait}.score.gz file.

  • ctrl_raw_score_<i_ctrl> : raw control scores, specified by --flag_return_ctrl_raw_score True.

  • ctrl_norm_score_<i_ctrl> : normalized control scores, specified by --flag_return_ctrl_norm_score True.

<trait>.scdrs_group.<annot>#

Results for scDRS group-level analysis for a give trait and a given cell-group annotation (e.g., cell type). .tsv file.

  • <trait> : trait name consistent with <trait>.full_score.gz file.

  • <annot> : cell-annotation in adata.obs.columns, specified by group_analysis in CLI.

  • First column: different cell groups in adata.obs[<annot>].

  • n_cell: number of cells from the cell group.

  • n_ctrl: number of control gene sets.

  • assoc_mcp: MC p-value for cell group-disease association. Raw p-value without multiple testing adjustment.

  • assoc_mcz: MC z-score for cell group-disease association.

  • hetero_mcp: MC p-value for within-cell group heterogeneity in association with disease. Raw p-value without multiple testing adjustment.

  • hetero_mcz: MC z-score for within-cell group heterogeneity in association with disease.

Example <trait>.scdrs_group.<annot> file#

n_cell

n_ctrl

assoc_mcp

assoc_mcz

hetero_mcp

hetero_mcz

causal_cell

10.0

20.0

0.04761905

12.297529

1.0

1.0

non_causal_cell

20.0

20.0

0.9047619

-1.1364214

1.0

1.0

<trait>.scdrs_cell_corr#

Results for scDRS cell-level correlation analysis for a given trait. .tsv file.

  • <trait> : trait name consistent with <trait>.full_score.gz file.

  • First column: all cell-level variables, specified by specified by corr_analysis in CLI.

  • n_ctrl: number of control gene sets.

  • corr_mcp: MC p-value for cell-level variable association with disease. Raw p-value without multiple testing adjustment.

  • corr_mcz: MC z-score for cell-level variable association with disease.

Example <trait>.scdrs_cell_corr file#

n_cell

corr_mcp

corr_mcz

causal_variable

20.0

0.04761905

3.4574268

non_causal_variable

20.0

0.23809524

0.8974108

covariate

20.0

0.1904762

1.1220891

<trait>.scdrs_gene#

Results for scDRS gene-level correlation analysis for a given trait. .tsv file.

  • <trait> : trait name consistent with <trait>.full_score.gz file.

  • First column: genes in adata.var_names.

  • CORR: correlation with scDRS disease score across all cells in adata.

  • RANK: rank of correlation across genes (starting from 0).

Example <trait>.scdrs_gene file#

index

CORR

RANK

Serping1

0.314

0

Lmna

0.278

1