5. Hannum
Predictor CpGs |
71 |
Unit |
Year |
Target Tissue |
whole blood |
Target Population |
Adult |
Method |
Elastic Net regression. |
Reference |
|
Alias |
5.1. Usage
usage: epical Hannum [-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.
5.2. Example
$ epical Hannum Test1_blood_N20_EPICv1_beta.tsv.gz -m Test1_blood_N20_EPICv1_info.tsv -o Hannum
2024-01-08 09:01:53 [INFO] The prefix of output files is set to "Hannum".
2024-01-08 09:01:53 [INFO] Loading Hannum clock data ...
2024-01-08 09:01:53 [INFO] Clock's name: "Hannum"
2024-01-08 09:01:53 [INFO] Clock was trained from: "whole blood"
2024-01-08 09:01:53 [INFO] Clock's unit: "years"
2024-01-08 09:01:53 [INFO] Number of CpGs used: 71
...