Merge branch 'dev' of https://ghproxy.com/https://github.com/bigbio/q…

…uantms.io into dev
bigbio · Oct 2, 2023 · 57df6e1 · 57df6e1
2 parents b93fb05 + ccf1144
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diff --git a/docs/feature.rst b/docs/feature.rst
@@ -27,11 +27,11 @@ Peptide properties and columns:
 -  ``sequence``: The peptide’s sequence corresponding to the feature, this peptide sequence do not includes posttraslational modifications -> ``string``
 -  ``unique``: Indicates whether the peptide sequence is unique for this protein in respect to the searched database -> ``boolean (0/1)``
 -  ``modifications``: A list of modifications for a give peptide ``[modification1, modification2, ...]``. A modification should be
-   recorded as string like `modification definition <README.rst#modifications>`__-> ``list[string]``
+   recorded as string like :doc:`introduction#modifications` -> ``list[string]``
 -  ``charge``: The charge assigned by the search engine/software -> ``integer``
 -  ``calc_mass_to_charge``: The PSM’s calculated (theoretical) mass to charge (m/z) -> ``double``
 -  ``exp_mass_to_charge``: The PSM’s experimental mass to charge (m/z) -> ``double``
--  ``peptidoform``: Peptidoform of the PSM. See more `documentation here <Introduction.rst#peptidoform>`__. -> ``string``
+-  ``peptidoform``: Peptidoform of the PSM. See more :doc:`introduction#peptidoform` -> ``string``
 -  ``posterior_error_probability``: Posterior Error Probability score from quantms -> ``double``
 -  ``global_qvalue``: Global q-value for the feature for the peptide identification in the experiment -> ``double``
 -  ``is_decoy``: Indicates whether the peptide sequence (coming from the PSM) is decoy -> ``boolean (0/1)``

diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -1,14 +1,14 @@
 Introduction to quantms.io
 ======================================
 
-The ``.qms`` folder will contain multiple metadata files that will be
+The ``.qms`` folder will contain multiple files that will be
 used to describe the project, the samples, the data acquisition and the
-data processing. Each of these files will be described in the following
+data processing, in addition to the data files. Each of these files will be described in the following
 sections:
 
 -  :doc:`metadata`: A json file for metadata about the
    analyzed project
--  :doc:`ae` or :doc:`de`: A csv file based on the MSstats (TODO link) format for either absolute expression or
+-  :doc:`ae` or :doc:`de`: A csv file based on the `MSstats <https://github.com/Vitek-Lab/MSstats>`_ format for either absolute expression or
    differential expression.
 
 Some general rules for all the files:
@@ -77,4 +77,4 @@ This concept is used in the following outputs:
 
 -  :doc:`psm`
 -  :doc:`feature`
--  :doc:`peptide`
+-  :doc:`peptide`