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cozygene · Dec 21, 2016 · 7f6e5e5 · 7f6e5e5
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diff --git a/docs/source/datamanagement.rst b/docs/source/datamanagement.rst
@@ -138,7 +138,7 @@ will remove all sites with mean methylation level above 0.8.
 
 **--rmxy**
 
-Filters out non-autosomal sites (sites in chromsomes X and Y). This argument assumes that the data were collected using the Illumina 450K array.
+Filters out non-autosomal sites (sites in chromsomes X and Y).
 
 For example::
 
@@ -151,7 +151,7 @@ will remove all non-autosomal sites from the data.
 
 **--rmns**
 
-Filters out cross-reactive (non specific) sites according to Chen et al. [1]_. This argument assumes that the data were collected using the Illumina 450K array.
+Filters out cross-reactive (non specific) sites according to Chen et al. [1]_ and McCartney et al. [2]_.
 
 For example::
 
@@ -164,7 +164,7 @@ will remove all non specific sites from the data.
 
 **--rmpoly**
 
-Filters out polymorphic sites according to Chen et al. [1]_. This argument assumes that the data were collected using the Illumina 450K array.
+Filters out polymorphic sites according to Chen et al. [1]_ and McCartney et al. [2]_.
 
 For example::
 
@@ -184,3 +184,5 @@ will remove all polymorphic sites from the data.
 
 
 .. [1] Chen, Yi-an, Mathieu Lemire, Sanaa Choufani, Darci T. Butcher, Daria Grafodatskaya, Brent W. Zanke, Steven Gallinger, Thomas J. Hudson, and Rosanna Weksberg. "Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray." Epigenetics 8, no. 2 (2013): 203-209.
+
+.. [2] McCartney, Daniel L., Rosie M. Walker, Stewart W. Morris, Andrew M. McIntosh, David J. Porteous, and Kathryn L. Evans. "Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip." Genomics Data 9 (2016): 22-24.
diff --git a/docs/source/howtocite.rst b/docs/source/howtocite.rst
@@ -6,10 +6,16 @@ If you use GLINT in any published work, please cite the paper describing it (**c
 
 In addition:
 
-- If you use the `--rmns`_ argument or the `--rmpoly`_ argument please also cite:
+- If you use the `--rmns`_ argument or the `--rmpoly`_ argument please also cite the followings.
+
+For 450K data:
 
 Chen, Yi-an, Mathieu Lemire, Sanaa Choufani, Darci T. Butcher, Daria Grafodatskaya, Brent W. Zanke, Steven Gallinger, Thomas J. Hudson, and Rosanna Weksberg. "Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray." Epigenetics 8, no. 2 (2013): 203-209.
 
+and for 850K (EPIC) data:
+
+McCartney, Daniel L., Rosie M. Walker, Stewart W. Morris, Andrew M. McIntosh, David J. Porteous, and Kathryn L. Evans. "Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip." Genomics Data 9 (2016): 22-24.
+
 - If you use the `--refactor`_ argument please also cite:
 
 Rahmani, Elior, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh et al. "Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies." Nature methods 13, no. 5 (2016): 443-445.

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -7,7 +7,7 @@
 Documentation and a quick start tutorial: GLINT!
 ================================================
 
-GLINT is a user-friendly command-line tool for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays (27K, 450K and EPIC). GLINT allows to easily run a pipeline of Epigenome-Wide Association Study (EWAS) under different models while accounting for known confounders in methylation data.
+GLINT is a user-friendly command-line tool for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays (27K, 450K and 850K/EPIC). GLINT allows to easily run a pipeline of Epigenome-Wide Association Study (EWAS) under different models while accounting for known confounders in methylation data.
 
 
 Getting GLINT:

diff --git a/docs/source/popstructure.rst b/docs/source/popstructure.rst
@@ -31,6 +31,8 @@ will compute the EPISTRUCTURE components of the data.
 
 .. note:: EPISTRUCTURE leverages polymorphic sites in order to capture the genetic and therefore the ancesty information in the data better. Therefore, we recommend to avoid removing polymorphic sites (`--rmpoly`_) before applying EPISTRUCTURE.
 
+.. note:: In case of data from heterogeneous source (e.g., blood), we suggest to account for type composition (see `--covar`_).
+
 .. note:: Use `--epi`_ together with `--gsave`_ in order to generate a new version of GLINT files with the computed EPISTRUCTURE components (these will be included in the *datafile.samples.txt* file).
 
 .. note:: Use `--out`_ in order to change the default output name.

diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
@@ -122,7 +122,7 @@ Finally, in our example we found a single significant association in chromosome
 |
 
 
-.. _here: https://github.com/cozygene/glint/releases/download/1.0.0/Tutorial_files.zip
+.. _here: https://github.com/cozygene/glint/releases/download/1.0.2/Tutorial_files.zip
 
 .. _download GLINT: download.html
 
@@ -157,7 +157,7 @@ Finally, in our example we found a single significant association in chromosome
 
 
 
-.. citations are in Chcago format
+.. citations are in Chicago format
 
 .. [1] Rahmani, Elior, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh et al. "Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies." Nature methods 13, no. 5 (2016): 443-445.
 .. [2] Jaffe, Andrew E., and Rafael A. Irizarry. "Accounting for cellular heterogeneity is critical in epigenome-wide association studies." Genome biology 15, no. 2 (2014): 1.

diff --git a/docs/source/versions.rst b/docs/source/versions.rst
@@ -5,6 +5,15 @@ Versions
 The latest version of GLINT is available on github `here`_.
 Below are details about each of the versions released so far.
 
+GLINT 1.0.2
+^^^^^^^^^^^
+*December 21, 2016*
+
+* Updated support for the Illumina EPIC array
+
+* The following arguments were updated: `--rmpoly`_, `--rmns`_
+
+
 GLINT 1.0.1
 ^^^^^^^^^^^
 *December 8, 2016*
@@ -28,3 +37,5 @@ The first release of GLINT!
 
 .. _--refactor: tissueheterogeneity.html#refactor
 .. _--houseman: tissueheterogeneity.html#houseman
+.. _--rmpoly: datamanagement.html#rmpoly
+.. _--rmns: datamanagement.html#rmns