added logo to README

README.Rmd

@@ -1,4 +1,5 @@
 ---
+title: "<img src='man/figures/scLANE_logo.png' align='right' height='20%' width='20%'/>"
 output: 
   github_document:
     toc: true
@@ -22,8 +23,6 @@ knitr::opts_chunk$set(warning = FALSE,
                       fig.height = 4)
 ```
 
-# `scLANE`
-
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README.md

@@ -1,7 +1,8 @@
+<img src='man/figures/scLANE_logo.png' align='right' height='20%' width='20%'/>
+================
 
-- [`scLANE`](#sclane)
-  - [Installation](#installation)
-  - [Model structure](#model-structure)
+- [Installation](#installation)
+- [Model structure](#model-structure)
 - [Usage](#usage)
   - [Libraries](#libraries)
   - [Input data](#input-data)
@@ -13,9 +14,6 @@
 - [References](#references)
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-
-# `scLANE`
-
 <!-- badges: start -->
 
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@@ -173,7 +171,7 @@ scLANE_models_glm <- testDynamic(sim_data,
 #> Registered S3 method overwritten by 'bit':
 #>   method   from  
 #>   print.ri gamlss
-#> scLANE testing in GLM mode completed for 100 genes across 1 lineage in 16.068 secs
+#> scLANE testing in GLM mode completed for 100 genes across 1 lineage in 26.604 secs
 ```
 
 After the function finishes running, we use `getResultsDE()` to generate
@@ -194,10 +192,10 @@ select(scLANE_res_glm, Gene, Lineage, Test_Stat, P_Val, P_Val_Adj, Gene_Dynamic_
 | Gene   | Lineage | LRT stat. | P-value | Adj. p-value | Predicted dynamic status |
 |:-------|:--------|----------:|--------:|-------------:|-------------------------:|
 | MFSD2B | A       |   217.016 |   0.000 |        0.000 |                        1 |
-| LGR4   | A       |     6.685 |   0.035 |        1.000 |                        0 |
-| UAP1L1 | A       |     9.882 |   0.007 |        0.365 |                        0 |
+| NLGN4Y | A       |     6.471 |   0.039 |        1.000 |                        0 |
+| UAP1L1 | A       |     9.882 |   0.007 |        0.357 |                        0 |
 | TMCO3  | A       |   167.764 |   0.000 |        0.000 |                        1 |
-| MRTO4  | A       |     4.771 |   0.092 |        1.000 |                        0 |
+| ZBTB43 | A       |     4.538 |   0.103 |        1.000 |                        0 |
 
 ### GEE mode
 
@@ -220,7 +218,7 @@ scLANE_models_gee <- testDynamic(sim_data,
                                  cor.structure = "ar1", 
                                  n.cores = 6L, 
                                  verbose = FALSE)
-#> scLANE testing in GEE mode completed for 100 genes across 1 lineage in 46.169 secs
+#> scLANE testing in GEE mode completed for 100 genes across 1 lineage in 1.499 mins
 ```
 
 We again generate the table of DE test results. The variance of the
@@ -239,10 +237,10 @@ select(scLANE_res_gee, Gene, Lineage, Test_Stat, P_Val, P_Val_Adj, Gene_Dynamic_
 | Gene  | Lineage | Wald stat. | P-value | Adj. p-value | Predicted dynamic status |
 |:------|:--------|-----------:|--------:|-------------:|-------------------------:|
 | BAD   | A       | 159682.044 |       0 |            0 |                        1 |
-| RPL29 | A       |     32.647 |       0 |            0 |                        1 |
+| TBCC  | A       |     31.307 |       0 |            0 |                        1 |
 | HOXC8 | A       |         NA |      NA |           NA |                        0 |
-| DDX41 | A       |   4216.586 |       0 |            0 |                        1 |
-| PFDN2 | A       |   2362.431 |       0 |            0 |                        1 |
+| NPC2  | A       |   3698.406 |       0 |            0 |                        1 |
+| MPG   | A       |   2270.035 |       0 |            0 |                        1 |
 
 ### GLMM mode
 
@@ -266,7 +264,7 @@ scLANE_models_glmm <- testDynamic(sim_data,
                                   id.vec = sim_data$subject, 
                                   n.cores = 6L, 
                                   verbose = FALSE)
-#> scLANE testing in GLMM mode completed for 100 genes across 1 lineage in 2.248 mins
+#> scLANE testing in GLMM mode completed for 100 genes across 1 lineage in 3.386 mins
 ```
 
 **Note:** The GLMM mode is still under development, as we are working on
@@ -289,8 +287,8 @@ select(scLANE_res_glmm, Gene, Lineage, Test_Stat, P_Val, P_Val_Adj, Gene_Dynamic
 | Gene    | Lineage | LRT stat. | P-value | Adj. p-value | Predicted dynamic status |
 |:--------|:--------|----------:|--------:|-------------:|-------------------------:|
 | VDAC1   | A       |   151.417 |       0 |            0 |                        1 |
-| KLHDC10 | A       |   122.491 |       0 |            0 |                        1 |
-| ZNF575  | A       |        NA |      NA |           NA |                        0 |
+| KLHDC10 | A       |   121.011 |       0 |            0 |                        1 |
+| NOP14   | A       |        NA |      NA |           NA |                        0 |
 | BCAT1   | A       |        NA |      NA |           NA |                        0 |
 | TSPAN1  | A       |    78.597 |       0 |            0 |                        1 |