fix: add missing lines

data-representation.qmd

@@ -1166,6 +1166,8 @@ distribution, e.g. when calculating distance-dependent genomic interaction
 frequency. 
 
 ```{r}
+pairsFile(yeast_hic) <- pairsf
+
 pairsFile(yeast_hic)
 
 readLines(pairsFile(yeast_hic), 25)

disseminating.qmd

@@ -219,9 +219,6 @@ fourDNData(experimentSetAccession = '4DNES25ABNZ1', type = 'compartments') |>
 
 ### Querying a complete experiment dataset
 
-Rather than querying each genomic file independently, one can automatically 
-fetch all the files associated with a given `experiment
-
 Rather than importing multiple files corresponding to a single experimentSet 
 accession ID one by one, one can import all the available files associated with 
 a experimentSet accession ID into a `HiCExperiment` object by using the 

interactions-centric.qmd

@@ -281,6 +281,12 @@ contact frequencies along a given chromosome in different samples.
 
 :::{.column-page-right}
 ```{r fig.asp = .4, out.width = '100%'}
+eco1_hic <- import(
+    CoolFile(HiContactsData('yeast_eco1', 'mcool')), 
+    focus = 'II', 
+    resolution = 2000
+)
+eco1_pairsf <- HiContactsData('yeast_eco1', 'pairs.gz')
 pairsFile(eco1_hic) <- eco1_pairsf
 eco1_scalo <- scalogram(eco1_hic) 
 merged_scalo <- rbind(

interoperability.qmd

@@ -65,6 +65,7 @@ remotes::install_github('TaoYang-dev/hicrep')
 In order to use `hicrep`, we first need to create two `HiCExperiment` objects. 
 
 ```{r eval = FALSE}
+library(InteractionSet)
 library(HiCExperiment)
 library(HiContactsData)
 
@@ -112,6 +113,7 @@ Manipulate a `HiCExperiment` object to coerce it into such structure is straight
 ```{r}
 library(dplyr)
 library(tidyr)
+library(purrr)
 hics <- list(
     "wt" = import(coolf_wt, format = 'cool'),
     "eco1" = import(coolf_eco1, format = 'cool')