diff --git a/articles/echodata.html b/articles/echodata.html index 8ca28c0..28e36d2 100644 --- a/articles/echodata.html +++ b/articles/echodata.html @@ -89,7 +89,7 @@


-Most recent update: Oct-20-2023
+Most recent update: Nov-17-2023

Source: vignettes/echodata.Rmd @@ -112,7 +112,7 @@

Nalls 2019
 fullSS_Nalls2019 <- echodata::example_fullSS(dataset = "Nalls2019")
-
## Writing file to ==> /tmp/Rtmp1brtKX/nalls2019.fullSS_subset.tsv
+
## Writing file to ==> /tmp/RtmpdAsvXH/nalls2019.fullSS_subset.tsv

Kunkle 2019 @@ -121,7 +121,7 @@

Kunkle 2019
 fullSS_Kunkle2019 <- echodata::example_fullSS(dataset = "Kunkle2019")

-
## Writing file to ==> /tmp/Rtmp1brtKX/kunkle2019.fullSS_subset.tsv
+
## Writing file to ==> /tmp/RtmpdAsvXH/kunkle2019.fullSS_subset.tsv
@@ -129,8 +129,8 @@

Session Info
 utils::sessionInfo()

-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-08 r85496)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -152,29 +152,29 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] echodata_0.99.17 BiocStyle_2.29.2
+## [1] echodata_0.99.17 BiocStyle_2.31.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] tidyr_1.3.0         sass_0.4.7          utf8_1.2.3         
-##  [4] generics_0.1.3      stringi_1.7.12      hms_1.1.3          
-##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.22      
+##  [1] tidyr_1.3.0         sass_0.4.7          utf8_1.2.4         
+##  [4] generics_0.1.3      stringi_1.8.1       hms_1.1.3          
+##  [7] digest_0.6.33       magrittr_2.0.3      evaluate_0.23      
 ## [10] bookdown_0.36       fastmap_1.1.1       R.oo_1.25.0        
-## [13] rprojroot_2.0.3     jsonlite_1.8.7      R.utils_2.12.2     
+## [13] rprojroot_2.0.4     jsonlite_1.8.7      R.utils_2.12.2     
 ## [16] zip_2.3.0           BiocManager_1.30.22 purrr_1.0.2        
 ## [19] fansi_1.0.5         textshaping_0.3.7   jquerylib_0.1.4    
-## [22] cli_3.6.1           rlang_1.1.1         R.methodsS3_1.8.2  
-## [25] cachem_1.0.8        yaml_2.3.7          tools_4.3.1        
-## [28] parallel_4.3.1      tzdb_0.4.0          memoise_2.0.1      
+## [22] cli_3.6.1           rlang_1.1.2         R.methodsS3_1.8.2  
+## [25] cachem_1.0.8        yaml_2.3.7          tools_4.4.0        
+## [28] parallel_4.4.0      tzdb_0.4.0          memoise_2.0.1      
 ## [31] dplyr_1.1.3         DT_0.30             vctrs_0.6.4        
-## [34] R6_2.5.1            lifecycle_1.0.3     stringr_1.5.0      
+## [34] R6_2.5.1            lifecycle_1.0.4     stringr_1.5.1      
 ## [37] fs_1.6.3            htmlwidgets_1.6.2   ragg_1.2.6         
 ## [40] pkgconfig_2.0.3     desc_1.4.2          pkgdown_2.0.7      
 ## [43] bslib_0.5.1         pillar_1.9.0        openxlsx_4.2.5.2   
 ## [46] data.table_1.14.8   glue_1.6.2          Rcpp_1.0.11        
-## [49] systemfonts_1.0.5   xfun_0.40           tibble_3.2.1       
-## [52] tidyselect_1.2.0    knitr_1.44          htmltools_0.5.6.1  
+## [49] systemfonts_1.0.5   xfun_0.41           tibble_3.2.1       
+## [52] tidyselect_1.2.0    knitr_1.45          htmltools_0.5.7    
 ## [55] rmarkdown_2.25      piggyback_0.1.5     readr_2.1.4        
-## [58] compiler_4.3.1

+## [58] compiler_4.4.0
diff --git a/articles/echolocatoR_Finemapping_Portal.html b/articles/echolocatoR_Finemapping_Portal.html index c846804..068ea40 100644 --- a/articles/echolocatoR_Finemapping_Portal.html +++ b/articles/echolocatoR_Finemapping_Portal.html @@ -89,7 +89,7 @@


-Updated: Oct-20-2023
+Updated: Nov-17-2023

Source: vignettes/echolocatoR_Finemapping_Portal.Rmd @@ -298,7 +298,7 @@

Query portalGWAS Nalls23andMe_2019 BST1 -/tmp/RtmpnFwKog/GWAS/Nalls23andMe_2019/BST1/multi_finemap/BST1.UKB.multi_finemap.csv.gz +/tmp/RtmpLFNqKd/GWAS/Nalls23andMe_2019/BST1/multi_finemap/BST1.UKB.multi_finemap.csv.gz www/data/GWAS/Nalls23andMe_2019/CHRNB1/multi_finemap/CHRNB1.UKB.multi_finemap.csv.gz @@ -313,7 +313,7 @@

Query portalGWAS Nalls23andMe_2019 CHRNB1 -/tmp/RtmpnFwKog/GWAS/Nalls23andMe_2019/CHRNB1/multi_finemap/CHRNB1.UKB.multi_finemap.csv.gz +/tmp/RtmpLFNqKd/GWAS/Nalls23andMe_2019/CHRNB1/multi_finemap/CHRNB1.UKB.multi_finemap.csv.gz www/data/GWAS/Nalls23andMe_2019/LRRK2/multi_finemap/LRRK2.UKB.multi_finemap.csv.gz @@ -328,7 +328,7 @@

Query portalGWAS Nalls23andMe_2019 LRRK2 -/tmp/RtmpnFwKog/GWAS/Nalls23andMe_2019/LRRK2/multi_finemap/LRRK2.UKB.multi_finemap.csv.gz +/tmp/RtmpLFNqKd/GWAS/Nalls23andMe_2019/LRRK2/multi_finemap/LRRK2.UKB.multi_finemap.csv.gz www/data/GWAS/Nalls23andMe_2019/BST1/LD/BST1.UKB.LD.csv.gz @@ -343,7 +343,7 @@

Query portalGWAS Nalls23andMe_2019 BST1 -/tmp/RtmpnFwKog/GWAS/Nalls23andMe_2019/BST1/LD/BST1.UKB.LD.csv.gz +/tmp/RtmpLFNqKd/GWAS/Nalls23andMe_2019/BST1/LD/BST1.UKB.LD.csv.gz www/data/GWAS/Nalls23andMe_2019/CHRNB1/LD/CHRNB1.UKB.LD.csv.gz @@ -358,7 +358,7 @@

Query portalGWAS Nalls23andMe_2019 CHRNB1 -/tmp/RtmpnFwKog/GWAS/Nalls23andMe_2019/CHRNB1/LD/CHRNB1.UKB.LD.csv.gz +/tmp/RtmpLFNqKd/GWAS/Nalls23andMe_2019/CHRNB1/LD/CHRNB1.UKB.LD.csv.gz www/data/GWAS/Nalls23andMe_2019/LRRK2/LD/LRRK2.UKB.LD.csv.gz @@ -373,7 +373,7 @@

Query portalGWAS Nalls23andMe_2019 LRRK2 -/tmp/RtmpnFwKog/GWAS/Nalls23andMe_2019/LRRK2/LD/LRRK2.UKB.LD.csv.gz +/tmp/RtmpLFNqKd/GWAS/Nalls23andMe_2019/LRRK2/LD/LRRK2.UKB.LD.csv.gz @@ -720,8 +720,8 @@

Session Info
 utils::sessionInfo()
-
## R version 4.3.1 (2023-06-16)
-## Platform: x86_64-pc-linux-gnu (64-bit)
+
## R Under development (unstable) (2023-11-08 r85496)
+## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.3 LTS
 ## 
 ## Matrix products: default
@@ -743,33 +743,33 @@ 
Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] echodata_0.99.17 BiocStyle_2.29.2
+## [1] echodata_0.99.17 BiocStyle_2.31.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] gtable_0.3.4        httr2_0.2.3         xfun_0.40          
+##  [1] gtable_0.3.4        httr2_1.0.0         xfun_0.41          
 ##  [4] bslib_0.5.1         ggplot2_3.4.4       htmlwidgets_1.6.2  
 ##  [7] gh_1.4.0            tzdb_0.4.0          yulab.utils_0.1.0  
-## [10] vctrs_0.6.4         tools_4.3.1         bitops_1.0-7       
-## [13] generics_0.1.3      curl_5.1.0          parallel_4.3.1     
+## [10] vctrs_0.6.4         tools_4.4.0         bitops_1.0-7       
+## [13] generics_0.1.3      curl_5.1.0          parallel_4.4.0     
 ## [16] tibble_3.2.1        fansi_1.0.5         pkgconfig_2.0.3    
 ## [19] R.oo_1.25.0         data.table_1.14.8   RColorBrewer_1.1-3 
-## [22] desc_1.4.2          lifecycle_1.0.3     compiler_4.3.1     
-## [25] stringr_1.5.0       dlstats_0.1.7       textshaping_0.3.7  
-## [28] munsell_0.5.0       htmltools_0.5.6.1   sass_0.4.7         
-## [31] RCurl_1.98-1.12     yaml_2.3.7          pillar_1.9.0       
+## [22] desc_1.4.2          lifecycle_1.0.4     compiler_4.4.0     
+## [25] stringr_1.5.1       dlstats_0.1.7       textshaping_0.3.7  
+## [28] munsell_0.5.0       htmltools_0.5.7     sass_0.4.7         
+## [31] RCurl_1.98-1.13     yaml_2.3.7          pillar_1.9.0       
 ## [34] pkgdown_2.0.7       jquerylib_0.1.4     tidyr_1.3.0        
 ## [37] R.utils_2.12.2      DT_0.30             cachem_1.0.8       
 ## [40] tidyselect_1.2.0    zip_2.3.0           digest_0.6.33      
-## [43] stringi_1.7.12      dplyr_1.1.3         purrr_1.0.2        
-## [46] bookdown_0.36       rprojroot_2.0.3     fastmap_1.1.1      
-## [49] grid_4.3.1          here_1.0.1          colorspace_2.1-0   
+## [43] stringi_1.8.1       dplyr_1.1.3         purrr_1.0.2        
+## [46] bookdown_0.36       rprojroot_2.0.4     fastmap_1.1.1      
+## [49] grid_4.4.0          here_1.0.1          colorspace_2.1-0   
 ## [52] cli_3.6.1           magrittr_2.0.3      piggyback_0.1.5    
-## [55] utf8_1.2.3          withr_2.5.1         readr_2.1.4        
+## [55] utf8_1.2.4          withr_2.5.2         readr_2.1.4        
 ## [58] rappdirs_0.3.3      scales_1.2.1        rmarkdown_2.25     
 ## [61] gitcreds_0.1.2      rvcheck_0.2.1       ragg_1.2.6         
 ## [64] R.methodsS3_1.8.2   hms_1.1.3           openxlsx_4.2.5.2   
-## [67] memoise_2.0.1       evaluate_0.22       echogithub_0.99.2  
-## [70] knitr_1.44          rworkflows_0.99.13  rlang_1.1.1        
+## [67] memoise_2.0.1       evaluate_0.23       echogithub_0.99.2  
+## [70] knitr_1.45          rworkflows_1.0.1    rlang_1.1.2        
 ## [73] Rcpp_1.0.11         glue_1.6.2          renv_1.0.3         
 ## [76] BiocManager_1.30.22 jsonlite_1.8.7      R6_2.5.1           
 ## [79] badger_0.2.3        systemfonts_1.0.5   fs_1.6.3

diff --git a/index.html b/index.html
index 6d043b9..ff72d65 100644
--- a/index.html
+++ b/index.html
@@ -85,7 +85,7 @@
 Authors: Brian Schilder, Jack Humphrey, Towfique Raj

-README updated: Oct-20-2023 +README updated: Nov-17-2023

diff --git a/pkgdown.yml b/pkgdown.yml index 7f1204c..f157128 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: echodata: echodata.html echolocatoR_Finemapping_Portal: echolocatoR_Finemapping_Portal.html -last_built: 2023-10-20T22:42Z +last_built: 2023-11-17T13:50Z diff --git a/reference/createDT.html b/reference/createDT.html index 01a43ad..4969535 100644 --- a/reference/createDT.html +++ b/reference/createDT.html @@ -96,8 +96,8 @@

See also

Examples

 
 echodata::createDT(dat = echodata::BST1)
-

-
+
+
diff --git a/reference/get_Nalls2019_loci.html b/reference/get_Nalls2019_loci.html index 28a5278..a708f80 100644 --- a/reference/get_Nalls2019_loci.html +++ b/reference/get_Nalls2019_loci.html @@ -122,9 +122,9 @@

Value

Examples

files <- get_Nalls2019_loci()
-#> Writing fine-mapped locus data ==> /tmp/RtmpmfAshP/Nalls23andMe_2019/BST1.multi_finemap.csv.gz
-#> Writing fine-mapped locus data ==> /tmp/RtmpmfAshP/Nalls23andMe_2019/LRRK2.multi_finemap.csv.gz
-#> Writing fine-mapped locus data ==> /tmp/RtmpmfAshP/Nalls23andMe_2019/MEX3C.multi_finemap.csv.gz
+#> Writing fine-mapped locus data ==> /tmp/RtmpLQCV4M/Nalls23andMe_2019/BST1.multi_finemap.csv.gz
+#> Writing fine-mapped locus data ==> /tmp/RtmpLQCV4M/Nalls23andMe_2019/LRRK2.multi_finemap.csv.gz
+#> Writing fine-mapped locus data ==> /tmp/RtmpLQCV4M/Nalls23andMe_2019/MEX3C.multi_finemap.csv.gz
diff --git a/reference/granges_to_bed.html b/reference/granges_to_bed.html index 676799e..06ed635 100644 --- a/reference/granges_to_bed.html +++ b/reference/granges_to_bed.html @@ -112,7 +112,7 @@

Examples

#> Converting dat to GRanges object. bed_path <- echodata::granges_to_bed(grlist = gr) #> Converting 1 GRanges object to separate BED files. -#> Saving BED file ==> /tmp/RtmpmfAshP/granges1.bed.txt +#> Saving BED file ==> /tmp/RtmpLQCV4M/granges1.bed.txt diff --git a/reference/merge_finemapping_results.html b/reference/merge_finemapping_results.html index 42e36ea..864a3a7 100644 --- a/reference/merge_finemapping_results.html +++ b/reference/merge_finemapping_results.html @@ -165,16 +165,16 @@

Examples

#> + Gathering all fine-mapping results from storage... #> + 3 multi-finemap files found. #> + Removing duplicate Multi-finemap files per locus. -#> + Importing results... RtmpmfAshP -#> + Importing results... RtmpmfAshP -#> + Importing results... RtmpmfAshP +#> + Importing results... RtmpLQCV4M +#> + Importing results... RtmpLQCV4M +#> + Importing results... RtmpLQCV4M #> Identifying Consensus SNPs... #> + support_thresh = 2 #> + Calculating mean Posterior Probability (mean.PP)... #> + 4 fine-mapping methods used. #> + 20 Credible Set SNPs identified. #> + 9 Consensus SNPs identified. -#> + Saving merged results ==> /tmp/RtmpmfAshP/file2ba21ae7a06fmerged_results.csv.gz +#> + Saving merged results ==> /tmp/RtmpLQCV4M/filebea03a55cf2amerged_results.csv.gz diff --git a/reference/read_parquet.html b/reference/read_parquet.html index 5fd3ccf..9773da7 100644 --- a/reference/read_parquet.html +++ b/reference/read_parquet.html @@ -114,7 +114,7 @@

Examples

dat <- echodata::BST1 path <- echodata::write_parquet(dat) #> Loading required namespace: arrow -#> Writing parquet file ==> /tmp/RtmpmfAshP/file2ba29f29e8a.parquet +#> Writing parquet file ==> /tmp/RtmpLQCV4M/filebea0448814ae.parquet #### Read the parquet file back into R #### dat2 <- echodata::read_parquet(path=path) #> Reading parquet file. diff --git a/reference/reassign_lead_snps.html b/reference/reassign_lead_snps.html index 6be50ba..5fe200b 100644 --- a/reference/reassign_lead_snps.html +++ b/reference/reassign_lead_snps.html @@ -111,8 +111,8 @@

Arguments

Examples

 
-merged_dat <- echodata::get_Nalls2019_merged()
-merged_dat2 <- echodata::reassign_lead_snps(merged_dat = merged_dat)
+merged_dat <- get_Nalls2019_merged()
+merged_dat2 <- reassign_lead_snps(merged_dat = merged_dat)
 #> Reassigning lead SNPs by: Dataset, Locus
diff --git a/reference/standardize.html b/reference/standardize.html index 15b0860..cbfb02c 100644 --- a/reference/standardize.html +++ b/reference/standardize.html @@ -169,7 +169,7 @@

Examples

#> ++ Ensuring 1 SNP per row and per genomic coordinate. #> ++ Removing extra whitespace #> + Standardized query: 6,211 SNPs x 28 columns. -#> ++ Saving standardized query ==> /tmp/RtmpmfAshP/BST1.tsv +#> ++ Saving standardized query ==> /tmp/RtmpLQCV4M/BST1.tsv diff --git a/reference/write_parquet.html b/reference/write_parquet.html index 457ff13..2c8fb0b 100644 --- a/reference/write_parquet.html +++ b/reference/write_parquet.html @@ -88,7 +88,7 @@

Arguments

Examples

dat <- echodata::BST1
 path <- echodata::write_parquet(dat = dat) 
-#> Writing parquet file ==> /tmp/RtmpmfAshP/file2ba265d6a9e8.parquet
+#> Writing parquet file ==> /tmp/RtmpLQCV4M/filebea073f8e778.parquet