dcalderon/rolypoly

Method for identifying trait-relevant gene annotations from GWAS summary statistics.

rolypoly

This package is meant to identify enrichment of SNP-trait association signal in functional annotations.

Install

install.packages("rolypoly")

Usage

For usage information see the introductory vignette. Additionally, refer to the manual for documentation of rolypoly functions.

Notes

• Still in early alpha phase.

Citation

The underlying model is described in: Calderon D (2017). Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. AJHG 10.1016/j.ajhg.2017.09.009

rolypoly's Issues

Error in rolypoly_link_blocks_and_gwas

Hi Diego,
We're trying to use rolypoly with a new data set - the example data set works fine, and we get the same answer as the vignette. However, we're running into an error with the new data. When I run rolypoly_roll, I get the following:

Reading expression set Data/eset.rds
Reading ad.rds
adding gwas
filtering out SNPs with MAF < 1%
adding block annotations
Error in names(chrom_gwas_list) <- paste("chr", names(chrom_gwas_list), :
'names' attribute [1] must be the same length as the vector [0]
Calls: rolypoly_roll -> rolypoly_link_blocks_and_gwas

Any ideas? (output of sessionInfo() below)
Thanks
Dan

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

Matrix products: default
BLAS: /nfs/teams/team170/Daniel/local/lib/R/lib/libRblas.so
LAPACK: /nfs/teams/team170/Daniel/local/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] bindrcpp_0.2 dplyr_0.7.4 Biobase_2.38.0
[4] BiocGenerics_0.24.0 rolypoly_0.1.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 bindr_0.1 magrittr_1.5
[4] munsell_0.4.3 lattice_0.20-35 colorspace_1.3-2
[7] R6_2.2.2 rlang_0.2.0 foreach_1.4.4
[10] plyr_1.8.4 grid_3.4.3 data.table_1.10.4-3
[13] gtable_0.2.0 iterators_1.0.9 lazyeval_0.2.1
[16] assertthat_0.2.0 tibble_1.4.2 Matrix_1.2-12
[19] ggplot2_2.2.1 codetools_0.2-15 glue_1.2.0
[22] compiler_3.4.3 pillar_1.2.1 scales_0.5.0
[25] pkgconfig_2.0.1

Error : Merging functional information returns empty object

Dear Author,
I have used rolyPoly before and has worked fine. Now I am trying to identify novel transcripts that are relevant to a trait, and hence have different IDs and not ENS gene IDs (anno_rp image attached). I don't know if this is the problem, whether rolyPoly is meant to analyze only genes. I get an error where after merging functional information, an empty object is returned (image attached). All the other file formats are fine, the reference builds match and the chromosome IDs match. Can you please help me with this?

Thanks,
Prakrithi

Add quick rolypoly tutorial

Manual

Since the package has been removed from CRAN , I am not able to access the manual or tutorials. Can I get them? I am trying to use this package and that would be of great help. Thanks in advance!

make repo public

Error in rolypoly_load_block_data

Hi,
We're getting an error in creating the rolypoly data object with the following message:

adding gwas
filtering out SNPs with MAF < 1%
adding block annotations
beginning processs of linking gwas and block annotations
merging functional information about blocks
Error in block$ld_matrix_squared %*% x :
requires numeric/complex matrix/vector arguments
Calls: rolypoly_roll ... rolypoly_load_block_data -> lapply -> FUN -> as.matrix
Execution halted

I'm not really sure how to debug this. Can anyone help?
Dan

upload repo to github

Don't forget to upload this at some point.

Rolling RolyPoly

Hello,

I am using RolyPoly for one of my projects but I am a little confused with the roly-poly_roll() function.
Well as given in the vignette the data we are passing in the ld_folder = ld_path and not ld_data. Is it a mistake in printing or it is the actual way of doing it?

Thank you

Running RolyPoly with the example data and not working

Hello,

Im trying to run RolyPoly with the example data available in this GitHub page and is not working. I don't know how to interpret the error Im getting.

Error in { : task 1 failed - "argument 'description' not valid"

The error comes when it tries to link the GWAS with the BLOCK annotation obj.

This is what Im running:

load("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/PAPERS/Integration_GWAS_scRNA-seq/ROLYPOLY/sim_gwas_data.rda")
load("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/PAPERS/Integration_GWAS_scRNA-seq/ROLYPOLY/sim_expression_data_normalized.rda")
load("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/PAPERS/Integration_GWAS_scRNA-seq/ROLYPOLY/sim_block_annotation.rda")
data <- readRDS("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/PAPERS/Integration_GWAS_scRNA-seq/ROLYPOLY/1.Rds")

rp <- rolypoly_roll(gwas_data =sim_gwas_data ,block_annotation = sim_block_annotation,block_data = sim_expression_data_normalized,ld_folder = data)

This is the part where the error is generate:

function (obj, ex) 
{
  e <- getDoSeq()
  environment(e$fun) <- new.env(parent = environment(e$fun))
  environment(e$fun)$.foreach_do <- TRUE
  e$fun(obj, substitute(ex), parent.frame(), e$data)
}

Also I tried in different system (MAC and LINUX) and still getting the same error
Hope someone can help : )

Thanks in advanced!

ERROR: "Error in { : task 1 failed - "cant find the function ".""

Hello!

I manage to run the example! But know Im having kind of the same issue with my data.

This is the error Im getting:

Error in { : task 1 failed - "cant find the function ".""

I get the error in the same place as the other one:

function (obj, ex) 
{
  e <- getDoSeq()
  environment(e$fun) <- new.env(parent = environment(e$fun))
  environment(e$fun)$.foreach_do <- TRUE
  e$fun(obj, substitute(ex), parent.frame(), e$data)
}

This is the data Im using:

gwas_data <- readRDS("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/4_Try_RolyPoly/gwas.filtrado.rds")
Gene_annotation <- readRDS("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/4_Try_RolyPoly/block.of.annotations.rds")
annonorm <- readRDS("3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/4_Try_RolyPoly/matriz.filtrada.tejidos.ENSG.rds")
ld_path <- "3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/3_Gwas/2_LD.Matrix/"

As suggested the ld_path now is a path and is going to a folder where I have a .rds object with the ld information for each chromosome.

Any idea where Im wrong?

Thanks in advanced,

ANE

Error while using a different LD file

Hi Diego,

I tried to run the rolypoly pipeline using the codes from this link: https://cran.r-project.org/web/packages/rolypoly/vignettes/intro.html

When I use the LD file (1.Rds) in the code it runs perfectly with the example sim files. But when I run the same with the LD files (1.Rds) provided in the link underneath the Linkage disequilibrium section (https://drive.google.com/file/d/0B_X6s0BThq9ZXzNNbjk3V2hNdlk/view?usp=sharing) I get an error saying:

adding gwas
filtering out SNPs with MAF < 1%
adding block annotations
beginning processs of linking gwas and block annotations
Error in { : task 1 failed - "invalid 'description' argument”

Could you help me out in debugging this?

Not able to instal RolyPoly

Hello,

Im trying to instal the packages and I get this error:

Warning in install.packages :
  package ‘rolypoly’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

Im working with the R version 4.1.3 (2022-03-10) and I have check the manual and tells that the package needs and R version >=3.1

Could someone one help me?

Thanks!

subscript out of bound

Hello Diego,

I'm trying to use rolypoly with my data. There was an error:

> rp <- rolypoly_roll(
+   gwas_data = dn0,
+   block_annotation = annot0,
+   block_data = ops0,
+   ld_folder = ld_path
+ )
adding gwas
filtering out SNPs with MAF < 1%
adding block annotations
beginning processs of linking gwas and block annotations
##------ Sun Mar 25 14:28:39 2018 ------## - starting blocks on chrom: 1
Error in { : task 2 failed - "subscript out of bounds"

How should I troubleshoot 'task 2 failed'? Thank you very much.

Best,
Phuwanat