crr-labels 1.0.0

FANTOM

To retrieve the FANTOM promoters you can proceed as follows:

from crr_labels import fantom

enhancers, promoters = fantom(
    cell_lines=["HelaS3", "GM12878"], # list of cell lines to be considered.
    window_size=200, # window size to use for the various regions.
    genome = "hg19", # considered genome version. Currently supported only "hg19".
    center_enhancers = "peak", # how to center the enhancer window, either around "peak" or the "center" of the region.
    enhancers_threshold = 0, # activation threshold for the enhancers.
    promoters_threshold = 5, # activation threshold for the promoters.
    drop_always_inactive_rows = True, # whetever to drop the rows where no activation is detected for every rows.
    nrows:int=None # the number of rows to read, usefull when testing pipelines for creating smaller datasets.
)

The library will download and parse the fantom project raw data and return two dataframes for the required cell lines. Consider reading the method docstring for more id-depth informations about the method.

The main steps are the following:

• The raw files are retrieved from the fantom dataset from the link specified in the fantom_data.json file

• The window for the enhancers and promoters are expanded or compressed to the given window size. In particular:

  • The enhancers window can either be centered on the region center with the “center” mode or around the “peak” with the “peak” mode.

  • The promoters window is upstream in the positive strand from the end of the promoter and downstream on the negative strand from the start of the promoter.

• When multiple experiments are present for a cell line, for instance for “HelaS3”, an average of the activation peaks is executed.

• Optionally (and by default) the rows that are always inactive for the chosen cell lines are dropped. You can specify this behaviour using the parameter “drop_always_inactive_rows”.

FANTOM