pandas_plink.read_plink¶

pandas_plink.read_plink(file_prefix, verbose=True)[source]¶

Read PLINK files into data frames.

Note

We suggest using read_plink1_bin() instead as it provides a clearer interface.

Examples

We have shipped this package with an example so can load and inspect by doing

>>> from os.path import join
>>> from pandas_plink import read_plink
>>> from pandas_plink import get_data_folder
>>> (bim, fam, bed) = read_plink(join(get_data_folder(), "data"), verbose=False)
>>> print(bim.head())
  chrom         snp       cm    pos a0 a1  i
0     1  rs10399749     0.00  45162  G  C  0
1     1   rs2949420     0.00  45257  C  T  1
2     1   rs2949421     0.00  45413  0  0  2
3     1   rs2691310     0.00  46844  A  T  3
4     1   rs4030303     0.00  72434  0  G  4
>>> print(fam.head())
        fid       iid    father    mother gender    trait  i
0  Sample_1  Sample_1         0         0      1    -9.00  0
1  Sample_2  Sample_2         0         0      2    -9.00  1
2  Sample_3  Sample_3  Sample_1  Sample_2      2    -9.00  2
>>> print(bed.compute())
[[2.00 2.00 1.00]
 [2.00 1.00 2.00]
 [ nan  nan  nan]
 [ nan  nan 1.00]
 [2.00 2.00 2.00]
 [2.00 2.00 2.00]
 [2.00 1.00 0.00]
 [2.00 2.00 2.00]
 [1.00 2.00 2.00]
 [2.00 1.00 2.00]]

The values of the bed matrix denote how many alleles a1 (see output of data frame bim) are in the corresponding position and individual. Notice the column i in bim and fam data frames. It maps to the corresponding position of the bed matrix:

>>> chrom1 = bim.query("chrom=='1'")
>>> X = bed[chrom1.i.values, :].compute()
>>> print(X)
[[2.00 2.00 1.00]
 [2.00 1.00 2.00]
 [ nan  nan  nan]
 [ nan  nan 1.00]
 [2.00 2.00 2.00]
 [2.00 2.00 2.00]
 [2.00 1.00 0.00]
 [2.00 2.00 2.00]
 [1.00 2.00 2.00]
 [2.00 1.00 2.00]]

It also allows the use of the wildcard character * for mapping multiple BED files at once: (bim, fam, bed) = read_plink("chrom*"). In this case, only one of the FAM files will be used to define sample information. Data from BIM and BED files are concatenated to provide a single view of the files.

Parameters

file_prefix (str) – Path prefix to the set of PLINK files. It supports loading many BED files at once using globstrings wildcard.
verbose (bool) – True for progress information; False otherwise.

Returns

alleles (pandas.DataFrame) – Alleles.
samples (pandas.DataFrame) – Samples.
genotypes (numpy.ndarray) – Genotype.