Local Data Loading#

This example loads data from a local file

Load up a local data file#

from biolearn.data_library import GeoData
from biolearn.util import get_test_data_file

#Files formatted as described in the standard https://bio-learn.github.io/methylation-standard.html will load correctly.

file_path = get_test_data_file("example_data.csv")
data = GeoData.from_methylation_matrix(file_path)

data.dnam
GSM3074480 GSM3074481 GSM3074482 GSM3074483
cpgSite
cg00000029 0.395 0.499 0.420 0.423
cg00000109 0.821 0.868 0.877 0.841
cg00000155 0.878 0.890 0.894 NaN


You can now use it like any other Biolearn dataset#

Quality Report Summary

------------------------------------------------
Sample Count: 4
Methylation Sites: 3
Missing Methylation Data: 1 (8.33%)
Samples With High Deviation: 0 (0.00%)
Methylation Sites With Over 20% of Reads Missing: 1 (33.33%)

Notes:
------------------------------------------------
- Your data set includes methylation sites that have over 20% of reads missing. Default imputation may replace the values for all reads from this site with a gold standard.

Total running time of the script: (0 minutes 0.421 seconds)

Estimated memory usage: 36 MB

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