Note
Go to the end to download the full example code or to run this example in your browser via Binder
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.
#Load will search for files names [name]_metadata.csv and [name]_methylation_part0.csv
file_path = get_test_data_file("")
data = GeoData.load_csv(file_path, "example")
data.dnam
Metadata is loaded if available#
You can now use it like any other Biolearn dataset#
data.quality_report().show()
Quality Report Summary
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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 0.482 seconds)
Estimated memory usage: 78 MB
