dnarecords.macros

DNARecords available macros.

Module Contents

Classes

DosageSparsityMacro

Pre-created methods to increase sparsity of your datasets
class dnarecords.macros.DosageSparsityMacro[source]

Pre-created methods to increase sparsity of your datasets

static supercharge_dosage_sparsity(mt: MatrixTable, info_score_threshold: float = 0.8, p_value_hwe_threshold: float = 1e-10, af_threshold: float = 0.001, sparse_threshold: float = 0.1) → MatrixTable[source]

Supercharges dosage sparsity based on info_score and variant_qc.

Assumes the input MatrixTable to have info_score and variant_qc row fields, and dosage entry field.

Note

It flips the dosage (2 - dosage) for those variants where alt allele is more frequent and includes a flag indicating whether the flip was done or not.

Example

import dnarecords as dr

hl = dr.helper.DNARecordsUtils.init_hail()
hl.utils.get_1kg('/tmp/1kg')
mt = hl.read_matrix_table('/tmp/1kg/1kg.mt')
mt = mt.annotate_rows(info_score=hl.agg.info_score(hl.pl_to_gp(mt.PL)))
mt = hl.variant_qc(mt)
mt = mt.annotate_entries(dosage=hl.pl_dosage(mt.PL))
mt = dr.macros.DosageSparsityMacro.supercharge_dosage_sparsity(mt)
mt.select_cols().select_rows('dosage_flip') \
   .select_entries('dosage','sparse_dosage').entries().show()

+---------------+------------+-------------+-----------+----------+---------------+
| locus         | alleles    | dosage_flip | s         |   dosage | sparse_dosage |
+---------------+------------+-------------+-----------+----------+---------------+
| locus<GRCh37> | array<str> |        bool | str       |  float64 |       float64 |
+---------------+------------+-------------+-----------+----------+---------------+
| 1:904165      | ["G","A"]  |       False | "HG00096" | 5,94e-02 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00099" | 3,97e-03 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00105" | 4,99e-03 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00118" | 7,88e-03 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00129" | 3,07e-02 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00148" | 7,36e-02 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00177" | 2,01e-01 |      2,01e-01 |
| 1:904165      | ["G","A"]  |       False | "HG00182" | 3,83e-02 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00242" | 3,07e-02 |      0,00e+00 |
| 1:904165      | ["G","A"]  |       False | "HG00254" | 1,26e-04 |      0,00e+00 |
+---------------+------------+-------------+-----------+----------+---------------+
Parameters

  • mt – a MatrixTable with info_score and variant_qc row fields, and dosage entry field.

  • info_score_threshold – rows with info_score.score below the threshold are filtered out.

  • p_value_hwe_threshold – rows with variant_qc.p_value_hwe below the threshold are filtered out.

  • af_threshold – rows with AF < af_threshold or AF > (1 - af_threshold) are filtered out.

  • sparse_threshold – those entries with dosage below the threshold are set dosage = 0.

Returns

a MatrixTable with above transformations done.

Return type

MatrixTable