Permalink
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
276 lines (178 sloc) 9.23 KB
.. index:: IC50

Data Format and Readers

CSV and TSV formats

The main formats used in GDSCTools are :term:`CSV`-based but :term:`TSV`-based formatted files may be accepted although not encouraged. The data files may be compressed using bz2, xz, gzip of zip methods. See Pandas documentation to know the exact list of authorised compression method. Note that files saved using GDSCTools will be saved in CSV format only.

GDSCTools provides tools to read different kind of structured CSV files. For instance in the ANOVA analysis, these 3 types of CSV-input files defined in :mod:`~gdsctools.readers` module) are used:

There are all based on the same :class:`~gdsctools.readers.Reader` class. Not a number values are encoded with the string NA or NaN. Besides, empty strings or fields made of spaces or tabs are also replaced by spaces.

Quote characters are also removed.

Warning

Some readers will use the name of the extensions to infer the separator so it is important that the extension reflects the content of the file. A compressed file named as e.g. ic50.csv.gz will therefore be interpreted as a CSV file.

Note

With CSV files, if a column's name is ambiguous in the header (i.e, contains already a comma), then it should be enclosed within double quotes to avoid ambiguities (e.g A,B should be "A,B"). See the :ref:`drug_decode` section for an example.

IC50

The specific format for the IC50 data is CSV file where the header must contain a column named COSMIC_ID. Other column should correspond to a given drug identifier (an integer). The order of the columns does not matter. So, each row contains the IC50s for a given COSMIC identifier.

Warning

the data read in the CSV file is not transformed. So, IC50 data should be logged data.

Note

The IC50 matrix can be populated with other data (e.g., AUCs).

Although the name in the header does not matter note that if one column's name starts with Drug then all columns that do not start with Drug are ignored (except the special column COSMIC_ID). This feature was implemented to account for old data files that stores all Drug identifiers and also all genomic features within a single file.

Here is an example of IC50 input:

COSMIC_ID, 1,           20,           40
111111,    0.5,         0.8,          10
222222,    1,           2,            10

The following old-style IC50 would be equivalent since (i) the last column is dropped (does not start with Drug) and (ii) the other column's names are transformed into integer keeping only the middle part:

COSMIC_ID, Drug_1_IC50, Drug_20_IC50, Drug_40_IC50, other
111111,    0.5,         0.8,          10,           10
222222,    1,           2,            10,           20

If you save that example in a file (or download it :download:`_static/ic50_tiny.csv`), you can read it with the :class:`~gdsctools.readers.IC50` class as follows:

>>> from gdsctools import IC50
>>> r = IC50('_static/ic50_tiny.csv')
>>> r.drugIds
[1, 20, 40]

Note

the columns' names should be identifiers (not drug names). There are two main reasons. The first one is that it allows us to keep anonymous all drug names and targets. The second reason is that many characteristics such as plate number and drug concentration may be associated with a drug identifier. This should be stored in a different table rather than in the name. It can then be handled and interpreted using the DrugDecode file (see below).

Note

column without a name are ignored.

.. seealso:: developers should look at the references for more
    functionalities of the :class:`~gdsctools.readers.IC50`
    class (e.g., filter by tissues, removing drugs, visualisation of IC50s).



Genomic Features

The ANOVA analysis computes the associations between the :term:`IC50` and genomic features. This is the second input data set required for instance in the ANOVA analysis. Be aware that in the ANOVA analysis, the intersection between the IC50 and GenomicFeatures is made on the COSMIC_ID: cell lines not found in both CSV files will be dropped.

In addition to the COSMIC identifiers, the genomic feature file should contain the following columns:

- TISSUE_FACTOR
- MSI_FACTOR
- MEDIA_FACTOR

If not provided, the tissue, :term:`MSI` and :term:`MEDIA` factors will not be taken into account in the regression analysis. If the :term:`TCGA` tissue is not provided, it is created and set to unidentified.

Note

.. versionchanged:: 0.9.11
    A column called 'Sample Name' was interpreted if found. This is not
    the case anymore. It is actually removed now.

All remaining columns are assumed to be genomic features.

Warning

In the current version, all columns starting with Drug_ are removed without warning.

Here is a simple example:

COSMIC_ID, TISSUE_FACTOR, MSI_FACTOR, BRAF_mut, gain_cna
111111, lung_NSCLC,  1, 1, 0
222222, prostate,    1, 0, 1

It can be saved and read as follows with the :class:`GenomicFeatures`

>>> from gdsctools import GenomicFeatures
>>> gf = GenomicFeatures('_static/gf_tiny.csv')
>>> gf
GenomicFeatures <Nc=2, Nf=2, Nt=2>

In GDSCTools, we provide a :download:`zipped Genomic Features file<../gdsctools/data/genomic_features.tsv.gz>`. It contains about 1000 cell lines and 47 genomic features (gene mutations). A more complex file tagged v17 is also provided with about 600 features :download:`v17 genomic feature <../gdsctools/data/genomic_features_v17.csv.gz>`.

Note that you may create instance of GenomicFeatures without input but a default data set is loaded (the subset aforementionned):

>>> from gdsctools import GenomicFeatures
>>> gf = GenomicFeatures()
>>> print(gf)
Genomic features distribution
Number of unique tissues 27
Here are the first 10 tissues: myeloma, nervous_system, soft_tissue, bone, lung_NSCLC, skin, Bladder, cervix, lung_SCLC, lung
MSI column: yes
MEDIA column: no
<BLANKLINE>
There are 47 unique features distributed as
- Mutation: 47
- CNA (gain): 0
- CNA (loss): 0

Combine IC50 and Genomic Features

Here is an example on how to plot histograms of IC50s grouped by tissues. For convenience, we keep only 9 tissues.

.. plot::
    :include-source:
    :width: 80%

    from gdsctools import *
    from numpy import mean
    ic50 = IC50(ic50_v17)
    gf = GenomicFeatures(gf_v17)
    # select tissue column in same order as those stored in IC50 dataframe
    tissues = gf.df.loc[ic50.df.index]['TISSUE_FACTOR']
    ic50.df['tissue'] = tissues

    # keep only 9 tissues
    tokeep = list(set(tissues))[0:9]
    ic50.df = ic50.df.query("tissue in @tokeep")

    # Group by tissues
    tt = ic50.df.groupby("tissue").aggregate(mean).transpose()
    #plot histogram of IC50 group by tissues
    tt.hist(bins=30, sharex=True)




Drug Decode

DrugDecode files are not required to perform the analysis. You may skip that section.

Drugs used in GDSCTools analysis may be public or not. In order to guarantee that drugs are kept anonymised (if not public), we enforce the CSV files that contains the IC50s to used drug identifiers instead of drug names.

When creating reports, the :ref:`data_packages` producer or owner or the drugs may want to decode the drug identifier. The information to perform that task is provided within the DrugDecode CSV file.

The :class:`~gdsctools.readers.DrugDecode` class reads a CSV file that contains information about a drug and its target(s). It must contain 3 columns named as follows:

DRUG_ID,    DRUG_NAME,  DRUG_TARGET
999,        Erlotinib,  EGFR
1039,       SL 0101-1,  "RSK, AURKB, PIM3"

Note the usage of quotes in the last row/last columns to avoid conflicts with the CSV format itself.

These columns will be used if provided:

- WEBRELEASE
- OWNED_BY

In addition, these columns may be populated for later use:

- CHEMSPIDER_ID
- PUBCHEM_ID
- CHEMBL_ID

An example can be read as follows:

>>> from gdsctools import DrugDecode, datasets
>>> drug_filename = datasets.testing.drug_test_csv.location
>>> dd = DrugDecode(drug_filename)
>>> dd.get_name(1047)
'Nutlin-3a'
>>> dd.df.loc[999]
CHEMBL_ID              NaN
CHEMSPIDER_ID          NaN
DRUG_NAME        Erlotinib
DRUG_TARGET           EGFR
OWNED_BY               NaN
PUBCHEM_ID             NaN
WEBRELEASE             NaN
Name: 999, dtype: object

DrugDecode files are not required for the analysis but are used by :class:`gdsctools.anova_report.ANOVAReport` to fill the HTML reports.

You can also run the analysis and set the drug names and target later on as follows using the :class:`~gdsctools.readers.drug_annotations` method:

from gdsctools import *
an = ANOVA(ic50_test)
an.anova_all()
results = an.anova_all()
dd = DrugDecode("v19_drug_decode.csv")
newdf = dd.drug_annotations(results.df)