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Update occurrences of 'feature' to 'gene' in docs which were missed p…
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…reviously.
pjbriggs committed Jan 28, 2016

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21 changes: 11 additions & 10 deletions README.rst
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RnaChipIntegrator: analysis of genomic features with peak data
==============================================================
RnaChipIntegrator: analysis of genes with peak data
===================================================

.. image:: https://readthedocs.org/projects/rnachipintegrator/badge/?version=latest
:target: https://rnachipintegrator.readthedocs.org
@@ -8,9 +8,9 @@ RnaChipIntegrator: analysis of genomic features with peak data
:target: https://travis-ci.org/fls-bioinformatics-core/RnaChipIntegrator

``RnaChipIntegrator`` is a utility that performs integrated analyses
of feature data (any set of genomic features, for example gene expression
data or canonical gene lists) with 'peak' data (a set of regions, for
example ChIP peaks) to identify the features to each peak, and vice versa.
of 'gene' data (a set of genes or other genomic features) with 'peak'
data (a set of regions, for example ChIP peaks) to identify the genes
nearest to each peak, and vice versa.

The program was originally written specifically for ChIP-Seq and RNA-Seq
data but works equally well for ChIP-chip and microarray expression data,
@@ -27,13 +27,14 @@ Install the latest version of the program from the Python Package Index

The simplest use of the program is::

RnaChipIntegrator FEATURES PEAKS
RnaChipIntegrator GENES PEAKS

where ``FEATURES`` and ``PEAKS`` are tab-delimited files containing
the genomic feature and peak data respecitively.
where ``GENES`` and ``PEAKS`` are tab-delimited files containing the
'gene' and 'peak' data respectively.

This will output two files with the nearest features for each peak,
and the nearest peaks for each feature.
This will output two files with the nearest genes for each peak
("peak-centric" analysis), and the nearest peaks for each gene
("gene-centric" analysis).

Full documentation can be found at ReadTheDocs:

6 changes: 3 additions & 3 deletions docs/index.rst
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RnaChipIntegrator: analyse 'genes' and 'peaks'
==============================================
RnaChipIntegrator: analyse 'genes' with 'peak' data
===================================================

``RnaChipIntegrator`` is a Python bioinformatics utility that performs
integrated analyses of 'gene' data (a set of genes or genomic features,
for example gene expression data or canonical gene lists) with 'peak' data
(a set of regions, for example ChIP peaks) to identify the nearest
features to each peak, and vice versa.
genes or features to each peak, and vice versa.

.. toctree::
:maxdepth: 2
12 changes: 6 additions & 6 deletions docs/outputs.rst
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@@ -42,8 +42,8 @@ TSS gene TSS position
TES gene TES position
dist_closest closest distance between peak and gene considering
all edges (zero if there is overlap)
dist_TSS distance between peak and feature TSS
dist_TES distance between peak and feature TES
dist_TSS distance between peak and gene TSS
dist_TES distance between peak and gene TES
direction 'U' if hit is upstream, 'D' if downstream, '.' if
overlapped
overlap_gene 1 if peak overlaps the gene, 0 if not
@@ -69,8 +69,8 @@ be filled with placeholders::
Use the ``--compact`` option to output all the genes for each peak
on a single line (:ref:`compact_output`).

Peaks associated with each feature ('gene-centric' output)
----------------------------------------------------------
Peaks associated with each gene ('gene-centric' output)
-------------------------------------------------------

By default the 'gene-centric' file has one line for each
gene/peak pair that is being reported, with the following
@@ -89,10 +89,10 @@ peak.start peak start position
peak.end peak end position
dist_closest closest distance between peak and gene considering
all edges (zero if there is overlap)
dist_TSS distance between peak and feature TSS
dist_TSS distance between peak and gene TSS
direction 'U' if hit is upstream, 'D' if downstream, '.' if
overlapped
in_the_gene 'YES' if peak overlaps the feaure, 'NO' if not
in_the_gene 'YES' if peak overlaps the gene, 'NO' if not
=============== ====================================================

Each gene will appear as many times as there are nearest peaks being
2 changes: 1 addition & 1 deletion docs/usage.rst
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@@ -18,7 +18,7 @@ This will produce two output files:

- ``GENES_peak_centric.txt``: reports the nearest genes
for each peak ('peak-centric' analysis)
- ``GENES_feature_centric.txt``: reports the nearest peaks
- ``GENES_gene_centric.txt``: reports the nearest peaks
for each gene ('gene-centric' analysis)

In both cases the files will contain one peak/gene pair per line

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