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<h1 class="title toc-ignore">Contrasts</h1>
<h4 class="author"><em>Yasin Kaymaz</em></h4>
<h4 class="date"><em>1/31/2019</em></h4>
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<p><strong>Last updated:</strong> 2019-03-04</p>
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<hr />
<p>Here, the purpose is to identify genes that are exclusively expressed in In6a and In6b cell population in contrast against the background cells.</p>
<pre><code>avg_logFC : log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group.
pct.1 : The percentage of cells where the gene is detected in the first group
pct.2 : The percentage of cells where the gene is detected in the second group
p_val_adj : Adjusted p-value, based on bonferroni correction using all genes in the dataset.</code></pre>
<div id="differential-expression-of-marker-genes-in-each-of-the-subsets" class="section level2">
<h2>Differential expression of marker genes in each of the subsets:</h2>
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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>avg_logFC<\/th>\n <th>pct.1<\/th>\n <th>pct.2<\/th>\n <th>p_val_adj<\/th>\n <th>cluster<\/th>\n <th>gene<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"deferRender":true,"scrollY":200,"scroller":true,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
</div>
<div id="pvalb-tac1-vs-gaba-clusters" class="section level2">
<h2>Pvalb-Tac1 vs GABA clusters</h2>
<p>Pvalb-Tac1 versus GABA clusters in PFC only. <strong>Pvalb-Tac1</strong> corresponds to In6b in Lake2018 while <strong>GABA clusters</strong> are In1a, In1b, In1c, In3, In4a, In4b, In6a, In7, In8.</p>
<pre><code>group1 = ("In6b")</code></pre>
<p>vs</p>
<pre><code>group2 = ("In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6a", "In7", "In8")</code></pre>
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<div id="in6-vs-all-others-in-ba10" class="section level2">
<h2>In6 vs all others in BA10</h2>
<p>In6 versus all remaining groups in BA10.</p>
<pre><code>group1 = ("In6a", "In6b")</code></pre>
<p>vs</p>
<pre><code>group2 = ("Ast", "End", "Mic", "Oli", "OPC", "Per","Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In7", "In8") </code></pre>
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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>avg_logFC<\/th>\n <th>pct.1<\/th>\n <th>pct.2<\/th>\n <th>p_val_adj<\/th>\n <th>gene<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"deferRender":true,"scrollY":200,"scroller":true,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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<div id="in6a-vs-all-others-in-ba10" class="section level2">
<h2>In6a vs all others in BA10</h2>
<p>In6a versus all remaining groups in BA10.</p>
<pre><code>group1 = ("In6a")</code></pre>
<p>vs</p>
<pre><code>group2 = ("Ast", "End", "Mic", "Oli", "OPC", "Per","Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6b", "In7", "In8")</code></pre>
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<div id="in6b-vs-all-others-in-ba10" class="section level2">
<h2>In6b vs all others in BA10</h2>
<p>In6b versus all remaining groups in BA10.</p>
<pre><code>group1 = ("In6b")</code></pre>
<p>vs</p>
<pre><code>group2 = ("Ast", "End", "Mic", "Oli", "OPC", "Per","Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6a", "In7", "In8")</code></pre>
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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>avg_logFC<\/th>\n <th>pct.1<\/th>\n <th>pct.2<\/th>\n <th>p_val_adj<\/th>\n <th>gene<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"deferRender":true,"scrollY":200,"scroller":true,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
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<div id="in6a-vs-all-other-neurons-in-ba10" class="section level2">
<h2>In6a vs all other Neurons in BA10</h2>
<p>In6a versus all remaining Neurons in BA10.</p>
<pre><code>group1 = ("In6a")</code></pre>
<p>vs</p>
<pre><code>group2 = ("Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6b", "In7", "In8")</code></pre>
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<div id="in6b-vs-all-other-neurons-in-ba10" class="section level2">
<h2>In6b vs all other Neurons in BA10</h2>
<p>In6b versus all remaining Neurons in BA10.</p>
<pre><code>group1 = ("In6b")</code></pre>
<p>vs</p>
<pre><code>group2 = ("Ex1", "Ex2", "Ex3e", "Ex4", "Ex5b", "Ex6a", "Ex6b", "Ex8","In1a", "In1b", "In1c", "In3", "In4a", "In4b", "In6a", "In7", "In8")</code></pre>
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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>avg_logFC<\/th>\n <th>pct.1<\/th>\n <th>pct.2<\/th>\n <th>p_val_adj<\/th>\n <th>gene<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"deferRender":true,"scrollY":200,"scroller":true,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
<p>.</p>
<p>.</p>
<p>.</p>
<p>.</p>
<p>.</p>
<p>.</p>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin17.5.0 (64-bit)
Running under: macOS 10.14.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 Seurat_2.3.3 Matrix_1.2-14 cowplot_0.9.3
[5] here_0.1 forcats_0.3.0 stringr_1.4.0 dplyr_0.7.6
[9] purrr_0.2.5 readr_1.1.1 tidyr_0.8.1 tibble_2.0.1
[13] tidyverse_1.2.1 DT_0.4 plotly_4.8.0 ggplot2_3.1.0
loaded via a namespace (and not attached):
[1] readxl_1.1.0 snow_0.4-3 backports_1.1.2
[4] Hmisc_4.1-1 workflowr_1.1.1 plyr_1.8.4
[7] igraph_1.2.1 lazyeval_0.2.1 splines_3.5.0
[10] crosstalk_1.0.0 digest_0.6.18 foreach_1.4.4
[13] htmltools_0.3.6 lars_1.2 gdata_2.18.0
[16] magrittr_1.5 checkmate_1.8.5 cluster_2.0.7-1
[19] mixtools_1.1.0 ROCR_1.0-7 modelr_0.1.2
[22] R.utils_2.6.0 colorspace_1.4-0 rvest_0.3.2
[25] haven_1.1.2 crayon_1.3.4 jsonlite_1.6
[28] bindr_0.1.1 survival_2.42-6 zoo_1.8-3
[31] iterators_1.0.10 ape_5.1 glue_1.3.0
[34] gtable_0.2.0 kernlab_0.9-26 prabclus_2.2-6
[37] DEoptimR_1.0-8 scales_1.0.0 mvtnorm_1.0-8
[40] Rcpp_1.0.0 metap_0.9 dtw_1.20-1
[43] xtable_1.8-2 viridisLite_0.3.0 htmlTable_1.12
[46] reticulate_1.9 foreign_0.8-70 bit_1.1-14
[49] proxy_0.4-22 mclust_5.4.1 SDMTools_1.1-221
[52] Formula_1.2-3 stats4_3.5.0 tsne_0.1-3
[55] htmlwidgets_1.2 httr_1.3.1 gplots_3.0.1
[58] RColorBrewer_1.1-2 fpc_2.1-11 acepack_1.4.1
[61] modeltools_0.2-22 ica_1.0-2 pkgconfig_2.0.2
[64] R.methodsS3_1.7.1 flexmix_2.3-14 nnet_7.3-12
[67] later_0.7.3 tidyselect_0.2.4 rlang_0.3.1
[70] reshape2_1.4.3 munsell_0.5.0 cellranger_1.1.0
[73] tools_3.5.0 cli_1.0.1 broom_0.5.0
[76] ggridges_0.5.0 evaluate_0.10.1 yaml_2.2.0
[79] knitr_1.20 bit64_0.9-7 fitdistrplus_1.0-9
[82] robustbase_0.93-1 caTools_1.17.1 RANN_2.6
[85] pbapply_1.4-0 nlme_3.1-137 mime_0.5
[88] whisker_0.3-2 R.oo_1.22.0 xml2_1.2.0
[91] hdf5r_1.0.1 compiler_3.5.0 rstudioapi_0.8
[94] png_0.1-7 stringi_1.2.4 lattice_0.20-35
[97] trimcluster_0.1-2 diffusionMap_1.1-0 pillar_1.3.1
[100] lmtest_0.9-36 data.table_1.11.4 bitops_1.0-6
[103] irlba_2.3.2 httpuv_1.4.4.2 R6_2.3.0
[106] latticeExtra_0.6-28 promises_1.0.1 KernSmooth_2.23-15
[109] gridExtra_2.3 codetools_0.2-15 MASS_7.3-50
[112] gtools_3.8.1 assertthat_0.2.0 rprojroot_1.3-2
[115] withr_2.1.2 diptest_0.75-7 parallel_3.5.0
[118] doSNOW_1.0.16 hms_0.4.2 grid_3.5.0
[121] rpart_4.1-13 class_7.3-14 rmarkdown_1.10
[124] segmented_0.5-3.0 Rtsne_0.15 git2r_0.23.0
[127] shiny_1.1.0 scatterplot3d_0.3-41 lubridate_1.7.4
[130] base64enc_0.1-3 </code></pre>
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