Add a figure for promoter logCPM filtering

thesis.lyx

@@ -5899,20 +5899,6 @@ trajectory
 \end_inset
 
 
-\end_layout
-
-\begin_layout Standard
-\begin_inset Flex TODO Note (inline)
-status open
-
-\begin_layout Plain Layout
-Which promoters were considered? Only ones with peaks? Only expressed genes?
- I don't recall exactly the filtering criteria.
-\end_layout
-
-\end_inset
-
-
 \end_layout
 
 \begin_layout Standard
@@ -5957,7 +5943,7 @@ TSS
 
 \end_inset
 
- with 21 windows.
+ with a total of 21 windows.
  Reads in each window for each 
 \begin_inset Flex Glossary Term
 status open
@@ -5980,6 +5966,47 @@ logCPM
 \end_inset
 
  as in the differential modification analysis.
+ An abundance threshold was chosen such that 99% of peak-containing promoters
+ have an average 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+logCPM
+\end_layout
+
+\end_inset
+
+ above this threshold (Figure 
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:Promoter-abundance-filtering"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+).
+ Then 
+\emph on
+all 
+\emph default
+promoters with an average 
+\begin_inset Flex Glossary Term
+status open
+
+\begin_layout Plain Layout
+logCPM
+\end_layout
+
+\end_inset
+
+ above this threshold were included, and all below that thereshold were
+ filtered out, regardless of whether they actually contained a called peak.
+ This ensures that even promoters containing undetected peaks will be included,
+ at the cost of likely including many promoters that do not contain any
+ true peak.
  Then, the 
 \begin_inset Flex Glossary Term
 status open
@@ -5990,9 +6017,9 @@ logCPM
 
 \end_inset
 
- values within each promoter were normalized to an average of zero, such
- that each window's normalized abundance now represents the relative read
- depth of that window compared to all other windows in the same promoter.
+ values of the bins within each promoter were normalized to an average of
+ zero, such that each window's normalized abundance now represents the relative
+ read depth of that window compared to all other windows in the same promoter.
  The normalized abundance values for each window in a promoter are collectively
  referred to as that promoter's 
 \begin_inset Quotes eld
@@ -6005,6 +6032,214 @@ relative coverage profile
 .
 \end_layout
 
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+afterpage{
+\end_layout
+
+\begin_layout Plain Layout
+
+
+\backslash
+begin{landscape}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+wide false
+sideways false
+status open
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me2-neighborhood-logCPM-filter.png
+	lyxscale 25
+	width 30col%
+	groupId nhood-filter-subfig
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+H3K4me2
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\begin_inset space \hfill{}
+\end_inset
+
+
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K4me3-neighborhood-logCPM-filter.png
+	lyxscale 25
+	width 30col%
+	groupId nhood-filter-subfig
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+H3K4me3
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\begin_inset space \hfill{}
+\end_inset
+
+
+\begin_inset Float figure
+wide false
+sideways false
+status collapsed
+
+\begin_layout Plain Layout
+\align center
+\begin_inset Graphics
+	filename graphics/CD4-csaw/ChIP-seq/H3K27me3-neighborhood-logCPM-filter.png
+	lyxscale 25
+	width 30col%
+	groupId nhood-filter-subfig
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+H3K27me3
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+\begin_inset Caption Standard
+
+\begin_layout Plain Layout
+\begin_inset Argument 1
+status collapsed
+
+\begin_layout Plain Layout
+Promoter abundance filtering for relative coverage profiles.
+\end_layout
+
+\end_inset
+
+
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:Promoter-abundance-filtering"
+
+\end_inset
+
+
+\series bold
+Promoter abundance filtering for relative coverage profiles.
+
+\series default
+ For each histone mark, a histogram of promoter logCPM values was plotted,
+ colored by whether each promoter contains a called peak.
+ The abundance filter for each histone mark (dotted vertical line) was set
+ such that 99% of peak-containing promoters (blue) are above the threshold,
+ and then all promoters above this threshold were included in downstream
+ analyses.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+end{landscape}
+\end_layout
+
+\begin_layout Plain Layout
+
+}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
 \begin_layout Subsection
 MOFA analysis of cross-dataset variation patterns
 \end_layout