Description Usage Arguments Value See Also Examples

Performs SNP-level circular genomic permutations. In each permutation,

the complete set of SNP association p-values are permuted by rotation

with respect to the SNPs' genomic locations.

Once these 'simulated' p-values are assigned,the proportion of SNPs per

set above a pre-defined threshold is calculated

1 2 3 | ```
snps_permutation(ordered_alldata = "", pers_ids = "", ntraits = "",
nper = 100, threshold = 0.05, saveto = "workspace",
gs_locs = "",envir ="")
``` |

`ordered_alldata` |
Return variable from "genome_order". Ordered genome and trait p-values |

`gs_locs` |
Return variable from "genome_order". SNP indexes |

`pers_ids` |
Return variable "per_ors" from "read2_paths". SNP indexes |

`ntraits` |
Traits INDEX to be analysed. Index according to "ordered_alldata". |

`nper` |
Number of permutations.Example: nper=1000 |

`threshold` |
Threshold to be set by the hypergeometric test. threshold=0.05 |

`saveto` |
Save permutation results to "workspace" OR "directory" |

`envir` |
R environment to save the Permutations to when saveto is set to "workspace" |

Returns "Permus_genesetsname" variables or files (permutation datasets).

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
# library(genomicper)
data(demo,SNPsAnnotation)
all_data <- read_pvals(data_name=demo,snps_ann=SNPsAnnotation)
genome_results <-genome_order(all_data=all_data)
# Results from genome_order
ordered_alldata <- genome_results$ordered_alldata
gs_locs <- genome_results$gs_locs
data(hsa00100,hsa00120,hsa00130,hsa00140,hsa00190,hsa02010)
paths_res <- read2_paths(ordered_alldata=ordered_alldata,gs_locs=gs_locs,
sets_from="workspace",sets_prefix="hsa",level="snp",envir=.GlobalEnv)
pers_ids <- paths_res$per_ors
pathways<- paths_res$pathways
# Create new environment to save the permutations to:
gper.env <- new.env()
# permutations
snps_permutation(ordered_alldata=ordered_alldata,pers_ids=pers_ids,
ntraits=c(7,9),nper=10,saveto="workspace",threshold=0.05,
gs_locs=gs_locs,envir = gper.env)
``` |

```
[1] "Arguments set:"
demo
SNPsAnnotation
[1] "workspace"
[1] "Number of SNPs without location and removed:0"
[1] "Arguments set:"
[1] "Ordered dataset: ordered_alldata"
[1] "Gene Annotations: gs_locs"
[1] "Gene-sets Location: workspace"
[1] "Gene-sets prefix: hsa"
[1] "Annotation level: snp"
[1] "Arguments"
[1] "Ordered dataset: ordered_alldata"
[1] "Indexes of SNP Annotations: pers_ids"
[1] "Indexes of Traits to Analyse: 7" "Indexes of Traits to Analyse: 9"
[1] "Traits: abpi" "Traits: abpildfa"
[1] "Number of permutations: 10"
[1] "Threshold: 0.05"
[1] "Permutation Results save to: workspace"
[1] "hsa00140"
```

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