Last updated on 2020-03-31 19:49:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 9.87 | 34.40 | 44.27 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 6.90 | 26.90 | 33.80 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 46.72 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 44.32 | OK | |||
| r-devel-windows-ix86+x86_64 | 0.1.0 | 11.00 | 50.00 | 61.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.1.0 | 9.00 | 49.00 | 58.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 9.06 | 33.65 | 42.71 | OK | |
| r-patched-solaris-x86 | 0.1.0 | 80.20 | OK | |||
| r-release-linux-x86_64 | 0.1.0 | 7.12 | 30.84 | 37.96 | OK | |
| r-release-windows-ix86+x86_64 | 0.1.0 | 12.00 | 63.00 | 75.00 | OK | |
| r-release-osx-x86_64 | 0.1.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.1.1 | 5.00 | 66.00 | 71.00 | ERROR | |
| r-oldrel-osx-x86_64 | 0.1.0 | OK |
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in 'getspres-Ex.R' failed
The error most likely occurred in:
> ### Name: plotspres
> ### Title: 'plotspres' generates forest plots showing _SPRE_ statistics.
> ### Aliases: plotspres plotspre forestspre spreforest plotspres.default
>
> ### ** Examples
>
> library(getspres)
>
>
> # Generate a forest plot showing SPRE statistics for variants in heartgenes214.
> # heartgenes214 is a case-control GWAS meta-analysis of coronary artery disease.
> # To learn more about the heartgenes214 dataset ?heartgenes214
>
> # Calculating SPRE statistics for 3 variants in heartgenes214
>
> heartgenes3 <- subset(heartgenes214,
+ variants %in% c("rs10139550", "rs10168194", "rs11191416"))
>
> getspres_results <- getspres(beta_in = heartgenes3$beta_flipped,
+ se_in = heartgenes3$gcse,
+ study_names_in = heartgenes3$studies,
+ variant_names_in = heartgenes3$variants)
>
> # Explore results generated by the getspres function
> str(getspres_results)
List of 4
$ number_variants: int 3
$ number_studies : int 48
$ spre_dataset :'data.frame': 143 obs. of 17 variables:
..$ beta : num [1:143] -0.2056 0.1058 0.0841 0.18 0.3271 ...
..$ se : num [1:143] 0.144 0.0778 0.0752 0.1286 0.1105 ...
..$ variant_names: Factor w/ 3 levels "rs10139550","rs10168194",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ study_names : Factor w/ 48 levels "01","02","03",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ study : Factor w/ 48 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ snp : Factor w/ 3 levels "1","2","3": 1 1 1 1 1 1 1 1 1 1 ...
..$ tau2 : num [1:143] 0.00211 0.00211 0.00211 0.00211 0.00211 ...
..$ I2 : num [1:143] 34.9 34.9 34.9 34.9 34.9 ...
..$ Q : num [1:143] 72.2 72.2 72.2 72.2 72.2 ...
..$ xb : num [1:143] 0.0631 0.0631 0.0631 0.0631 0.0631 ...
..$ xbse : num [1:143] 0.0121 0.0121 0.0121 0.0121 0.0121 ...
..$ xbu : num [1:143] 0.0383 0.0741 0.0688 0.0763 0.102 ...
..$ stdxbu : num [1:143] 0.0451 0.0406 0.0402 0.0446 0.0437 ...
..$ hat : num [1:143] 0.00626 0.01752 0.01842 0.00768 0.00999 ...
..$ rawresid : num [1:143] -0.2687 0.0427 0.021 0.1169 0.264 ...
..$ uncondse : num [1:143] 0.1507 0.0896 0.0873 0.136 0.1191 ...
..$ spre : num [1:143] -1.784 0.477 0.241 0.86 2.217 ...
$ call : language getspres.default(beta_in = heartgenes3$beta_flipped, se_in = heartgenes3$gcse, study_names_in = heartgenes3$| __truncated__
- attr(*, "class")= chr "getspres"
>
> # Retrieve number of studies and variants
> getspres_results$number_variants
[1] 3
> getspres_results$number_studies
[1] 48
>
> # Retrieve SPRE dataset
> df_spres <- getspres_results$spre_dataset
> head(df_spres)
beta se variant_names study_names study
rs10139550.rs10139550.01 -0.205650 0.14399623 rs10139550 01 1
rs10139550.rs10139550.02 0.105799 0.07784344 rs10139550 02 2
rs10139550.rs10139550.03 0.084100 0.07523906 rs10139550 03 3
rs10139550.rs10139550.04 0.180000 0.12857537 rs10139550 04 4
rs10139550.rs10139550.05 0.327100 0.11052377 rs10139550 05 5
rs10139550.rs10139550.06 0.152000 0.06835058 rs10139550 06 6
snp tau2 I2 Q xb xbse
rs10139550.rs10139550.01 1 0.002109174 34.87837 72.17264 0.06309822 0.012147
rs10139550.rs10139550.02 1 0.002109174 34.87837 72.17264 0.06309822 0.012147
rs10139550.rs10139550.03 1 0.002109174 34.87837 72.17264 0.06309822 0.012147
rs10139550.rs10139550.04 1 0.002109174 34.87837 72.17264 0.06309822 0.012147
rs10139550.rs10139550.05 1 0.002109174 34.87837 72.17264 0.06309822 0.012147
rs10139550.rs10139550.06 1 0.002109174 34.87837 72.17264 0.06309822 0.012147
xbu stdxbu hat rawresid
rs10139550.rs10139550.01 0.03828494 0.04512203 0.006264557 -0.26874822
rs10139550.rs10139550.02 0.07412354 0.04056819 0.017518916 0.04270078
rs10139550.rs10139550.03 0.06879911 0.04018658 0.018417818 0.02100178
rs10139550.rs10139550.04 0.07632546 0.04457099 0.007677144 0.11690178
rs10139550.rs10139550.05 0.10197000 0.04365680 0.009990319 0.26400178
rs10139550.rs10139550.06 0.09075049 0.03902777 0.021104352 0.08890178
uncondse spre
rs10139550.rs10139550.01 0.15065370 -1.7838806
rs10139550.rs10139550.02 0.08956130 0.4767771
rs10139550.rs10139550.03 0.08730716 0.2405504
rs10139550.rs10139550.04 0.13598989 0.8596358
rs10139550.rs10139550.05 0.11906775 2.2172400
rs10139550.rs10139550.06 0.08144585 1.0915446
>
> # Extract SPREs from SPRE dataset
> head(spres <- df_spres[, "spre"])
[1] -1.7838806 0.4767771 0.2405504 0.8596358 2.2172400 1.0915446
>
>
> # Generating forest plots showing SPREs for variants in heartgenes3
>
> # Forest plot with default settings
> # Tip: To store plots set save_plot = TRUE (useful when generating multiple plots)
> plotspres_res <- plotspres(beta_in = df_spres$beta,
+ se_in = df_spres$se,
+ study_names_in = as.character(df_spres$study_names),
+ variant_names_in = as.character(df_spres$variant_names),
+ spres_in = df_spres$spre,
+ save_plot = FALSE)
Error in update_tibble_attrs(x, ...) :
object 'tibble_update_attrs' not found
Calls: plotspres ... recycle_columns -> new_tibble -> update_tibble_attrs
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64