14. PedBE

Predictor CpGs

94

Unit

Year

Target Tissue

Buccal cells

Target Population

Children (0 to 20)

Method

Elastic Net regression

Reference

McEwen LM, et al., Proc Natl Acad Sci U S A. (2020).

Alias

14.1. Usage

usage: epical PedBE  [-h] [-o out_prefix] [-p PERCENT] [-d DELIMITER]
                     [-f {pdf,png}] [-m meta_file] [-l log_file]
                     [--impute {-1,0,1,2,3,4,5,6,7,8,9,10}] [-r ref_file]
                     [--debug] [--overwrite]
                     Input_file

positional arguments:
  Input_file            The input tabular structure file containing DNA
                        methylation data. This filemust have a header row,
                        which contains the names or labels for samples
                        Thefirst column of this file should contain CpG IDs.
                        The remaining cells in thefile should contain DNA
                        methylation beta values, represented as floating-
                        pointnumbers between 0 and 1. Use a TAB, comma, or any
                        other delimiter to separatethe columns. Use 'NaN' or
                        'NA' to represent missing values. This file can be a
                        regular text file or compressed file (".gz", ".Z",
                        ".z", ".bz", ".bz2", ".bzip2").

options:
  -h, --help            show this help message and exit
  -o out_prefix, --output out_prefix
                        The PREFIX of output files. If no PREFIX is provided,
                        the default prefix "clock_name_out" is used. The
                        generated output files include:
                        "<PREFIX>.DNAm_age.tsv": This file contains the
                        predicted DNAm age. "<PREFIX>.used_CpGs.tsv": This
                        file lists the CpGs that were used to calculate the
                        DNAm age. "<PREFIX>.missed_CpGs.txt": This file
                        provides a list of clock CpGs that were missed or
                        excluded from the input file. "<PREFIX>.coef.tsv":
                        This file contains a list of clock CpGs along with
                        their coefficients. The last column indicates whether
                        the CpG is included in the calculation.
                        "<PREFIX>.plots.R": This file is an R script used to
                        generate visualization plots.
                        "<PREFIX>.coef_plot.pdf": This file is the coefficient
                        plot in either PDF or PNG format.
  -p PERCENT, --percent PERCENT
                        The maximum allowable percentage of missing CpGs. Set
                        to 0.2 (20%) by default, which means that if more than
                        20% of the clock CpGs are missing, the estimation of
                        DNAm age cannot be performed.
  -d DELIMITER, --delimiter DELIMITER
                        Separator (usually TAB or comma) used in the input
                        file. If the separator is not provided, the program
                        will automatically detect the separator.
  -f {pdf,png}, --format {pdf,png}
                        Figure format of the output coef plot. It must be
                        "pdf" or "png". The default is "pdf".
  -m meta_file, --metadata meta_file
                        This file contains the meta information for each
                        sample. This file must have a header row, which
                        contains the names or labels for variables (such as
                        "Sex", "Age"). If the header row includes an "Age"
                        column, a scatter plot will be generated to display
                        the correlation between chronological age and
                        predicted DNAm age. The first column of this file
                        should contain sample IDs. The default value is None,
                        indicating that no meta information file is provided.
  -l log_file, --log log_file
                        This file is used to save the log information. By
                        default, if no file is specified (None), the log
                        information will be printed to the screen.
  --impute {-1,0,1,2,3,4,5,6,7,8,9,10}
                        The imputation method code must be one of the 12
                        digits including (-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
                        10). The interpretations are: -1: Remove CpGs with any
                        missing values. 0: Fill all missing values with '0.0'.
                        1: Fill all missing values with '1.0'. 2: Fill the
                        missing values with **column mean** 3: Fill the
                        missing values with **column median** 4: Fill the
                        missing values with **column min** 5: Fill the missing
                        values with **column max** 6: Fill the missing values
                        with **row mean** 7: Fill the missing values with
                        **row median** 8: Fill the missing values with **row
                        min** 9: Fill the missing values with **row max** 10:
                        Fill the missing values with **external reference** If
                        10 is specified, an external reference file must be
                        provided.
  -r ref_file, --ref ref_file
                        The external reference file contains two columns,
                        separated by either tabs or commas. The first column
                        represents the probe ID, while the second column
                        contains the corresponding beta values.
  --debug               If set, print detailed information for debugging.
  --overwrite           If set, over-write existing output files.

14.2. Example

$ epical PedBE Test2_blood_N80_450K_beta.tsv.gz -m Test2_blood_N80_450K_info.tsv -o PedBE_out

2024-01-22 11:33:09 [INFO]  The prefix of output files is set to "PedBE_out".
2024-01-22 11:33:09 [INFO]  Loading PedBE clock data ...
2024-01-22 11:33:09 [INFO]  Clock's name: "McEwen_PedBE"
2024-01-22 11:33:09 [INFO]  Clock was trained from: "buccal cells"
2024-01-22 11:33:09 [INFO]  Clock's unit: "years"
2024-01-22 11:33:09 [INFO]  Number of CpGs used: 94

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