xPierSNPsAdv: Function to prepare genetic predictors given a list of seed...

Description Usage Arguments Value Note See Also Examples

View source: R/xPierSNPsAdv.r

Description

xPierSNPsAdv is supposed to prepare genetic predictors given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values). Internally it calls xPierSNPs to prepare the distance predictor, the eQTL predictors (if required) and the HiC predictors (if required). It returns a list of class "pNode" objects.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
xPierSNPsAdv(
data,
include.LD = NA,
LD.customised = NULL,
LD.r2 = 0.8,
significance.threshold = 5e-05,
score.cap = 10,
distance.max = 2000,
decay.kernel = c("slow", "constant", "linear", "rapid"),
decay.exponent = 2,
GR.SNP = c("dbSNP_GWAS", "dbSNP_Common", "dbSNP_Single"),
GR.Gene = c("UCSC_knownGene", "UCSC_knownCanonical"),
include.TAD = c("none", "GM12878", "IMR90", "MSC", "TRO", "H1", "MES",
"NPC"),
include.eQTL = NA,
eQTL.customised = NULL,
include.HiC = NA,
cdf.function = c("empirical", "exponential"),
scoring.scheme = c("max", "sum", "sequential"),
network = c("STRING_highest", "STRING_high", "STRING_medium",
"STRING_low",
"PCommonsUN_high", "PCommonsUN_medium", "PCommonsDN_high",
"PCommonsDN_medium",
"PCommonsDN_Reactome", "PCommonsDN_KEGG", "PCommonsDN_HumanCyc",
"PCommonsDN_PID",
"PCommonsDN_PANTHER", "PCommonsDN_ReconX", "PCommonsDN_TRANSFAC",
"PCommonsDN_PhosphoSite", "PCommonsDN_CTD", "KEGG", "KEGG_metabolism",
"KEGG_genetic", "KEGG_environmental", "KEGG_cellular",
"KEGG_organismal",
"KEGG_disease", "REACTOME"),
STRING.only = c(NA, "neighborhood_score", "fusion_score",
"cooccurence_score",
"coexpression_score", "experimental_score", "database_score",
"textmining_score")[1],
weighted = FALSE,
network.customised = NULL,
seeds.inclusive = TRUE,
normalise = c("laplacian", "row", "column", "none"),
restart = 0.7,
normalise.affinity.matrix = c("none", "quantile"),
parallel = TRUE,
multicores = NULL,
verbose = TRUE,
verbose.details = FALSE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

data

a named input vector containing the sinificance level for nodes (dbSNP). For this named vector, the element names are dbSNP ID (or in the format such as 'chr16:28525386'), the element values for the significance level (measured as p-value or fdr). Alternatively, it can be a matrix or data frame with two columns: 1st column for dbSNP, 2nd column for the significance level

include.LD

additional SNPs in LD with Lead SNPs are also included. By default, it is 'NA' to disable this option. Otherwise, LD SNPs will be included based on one or more of 5 super-populations from 1000 Genomics Project data (phase 3). They are "AFR", "AMR", "EAS", "EUR", and "SAS". Explanations for population code can be found at http://www.1000genomes.org/faq/which-populations-are-part-your-study

LD.customised

a user-input matrix or data frame with 3 columns: 1st column for Lead SNPs, 2nd column for LD SNPs, and 3rd for LD r2 value. It is designed to allow the user analysing their pre-calculated LD info. This customisation (if provided) has the high priority over built-in LD SNPs

LD.r2

the LD r2 value. By default, it is 0.8, meaning that SNPs in LD (r2>=0.8) with input SNPs will be considered as LD SNPs. It can be any value from 0.8 to 1

significance.threshold

the given significance threshold. By default, it is set to NULL, meaning there is no constraint on the significance level when transforming the significance level of SNPs into scores. If given, those SNPs below this are considered significant and thus scored positively. Instead, those above this are considered insigificant and thus receive no score

score.cap

the maximum score being capped. By default, it is set to 10. If NULL, no capping is applied

distance.max

the maximum distance between genes and SNPs. Only those genes no far way from this distance will be considered as seed genes. This parameter will influence the distance-component weights calculated for nearby SNPs per gene

decay.kernel

a character specifying a decay kernel function. It can be one of 'slow' for slow decay, 'linear' for linear decay, and 'rapid' for rapid decay. If no distance weight is used, please select 'constant'

decay.exponent

an integer specifying a decay exponent. By default, it sets to 2

GR.SNP

the genomic regions of SNPs. By default, it is 'dbSNP_GWAS', that is, SNPs from dbSNP (version 146) restricted to GWAS SNPs and their LD SNPs (hg19). It can be 'dbSNP_Common', that is, Common SNPs from dbSNP (version 146) plus GWAS SNPs and their LD SNPs (hg19). Alternatively, the user can specify the customised input. To do so, first save your RData file (containing an GR object) into your local computer, and make sure the GR object content names refer to dbSNP IDs. Then, tell "GR.SNP" with your RData file name (with or without extension), plus specify your file RData path in "RData.location". Note: you can also load your customised GR object directly

GR.Gene

the genomic regions of genes. By default, it is 'UCSC_knownGene', that is, UCSC known genes (together with genomic locations) based on human genome assembly hg19. It can be 'UCSC_knownCanonical', that is, UCSC known canonical genes (together with genomic locations) based on human genome assembly hg19. Alternatively, the user can specify the customised input. To do so, first save your RData file (containing an GR object) into your local computer, and make sure the GR object content names refer to Gene Symbols. Then, tell "GR.Gene" with your RData file name (with or without extension), plus specify your file RData path in "RData.location". Note: you can also load your customised GR object directly

include.TAD

TAD boundary regions are also included. By default, it is 'none' to disable this option. Otherwise, inclusion of a TAD dataset to pre-filter SNP-nGene pairs (i.e. only those within a TAD region will be kept). TAD datasets can be one of "GM12878" (lymphoblast), "IMR90" (fibroblast), "MSC" (mesenchymal stem cell) ,"TRO" (trophoblasts-like cell), "H1" (embryonic stem cell), "MES" (mesendoderm) and "NPC" (neural progenitor cell). Explanations can be found at http://dx.doi.org/10.1016/j.celrep.2016.10.061

include.eQTL

the eQTL supported currently. By default, it is 'NA' to disable this option. Pre-built eQTL datasets are detailed in xDefineEQTL

eQTL.customised

a user-input matrix or data frame with 4 columns: 1st column for SNPs/eQTLs, 2nd column for Genes, 3rd for eQTL mapping significance level (p-values or FDR), and 4th for contexts (required even though only one context is input). Alternatively, it can be a file containing these 4 columns. It is designed to allow the user analysing their eQTL data. This customisation (if provided) will populate built-in eQTL data

include.HiC

genes linked to input SNPs are also included. By default, it is 'NA' to disable this option. Otherwise, those genes linked to SNPs will be included according to Promoter Capture HiC (PCHiC) datasets. Pre-built HiC datasets are detailed in xDefineHIC

cdf.function

a character specifying a Cumulative Distribution Function (cdf). It can be one of 'exponential' based on exponential cdf, 'empirical' for empirical cdf

scoring.scheme

the method used to calculate seed gene scores under a set of SNPs. It can be one of "sum" for adding up, "max" for the maximum, and "sequential" for the sequential weighting. The sequential weighting is done via: ∑_{i=1}{\frac{R_{i}}{i}}, where R_{i} is the i^{th} rank (in a descreasing order)

network

the built-in network. Currently two sources of network information are supported: the STRING database (version 10) and the Pathway Commons database (version 7). STRING is a meta-integration of undirect interactions from the functional aspect, while Pathways Commons mainly contains both undirect and direct interactions from the physical/pathway aspect. Both have scores to control the confidence of interactions. Therefore, the user can choose the different quality of the interactions. In STRING, "STRING_highest" indicates interactions with highest confidence (confidence scores>=900), "STRING_high" for interactions with high confidence (confidence scores>=700), "STRING_medium" for interactions with medium confidence (confidence scores>=400), and "STRING_low" for interactions with low confidence (confidence scores>=150). For undirect/physical interactions from Pathways Commons, "PCommonsUN_high" indicates undirect interactions with high confidence (supported with the PubMed references plus at least 2 different sources), "PCommonsUN_medium" for undirect interactions with medium confidence (supported with the PubMed references). For direct (pathway-merged) interactions from Pathways Commons, "PCommonsDN_high" indicates direct interactions with high confidence (supported with the PubMed references plus at least 2 different sources), and "PCommonsUN_medium" for direct interactions with medium confidence (supported with the PubMed references). In addition to pooled version of pathways from all data sources, the user can also choose the pathway-merged network from individual sources, that is, "PCommonsDN_Reactome" for those from Reactome, "PCommonsDN_KEGG" for those from KEGG, "PCommonsDN_HumanCyc" for those from HumanCyc, "PCommonsDN_PID" for those froom PID, "PCommonsDN_PANTHER" for those from PANTHER, "PCommonsDN_ReconX" for those from ReconX, "PCommonsDN_TRANSFAC" for those from TRANSFAC, "PCommonsDN_PhosphoSite" for those from PhosphoSite, and "PCommonsDN_CTD" for those from CTD. For direct (pathway-merged) interactions sourced from KEGG, it can be 'KEGG' for all, 'KEGG_metabolism' for pathways grouped into 'Metabolism', 'KEGG_genetic' for 'Genetic Information Processing' pathways, 'KEGG_environmental' for 'Environmental Information Processing' pathways, 'KEGG_cellular' for 'Cellular Processes' pathways, 'KEGG_organismal' for 'Organismal Systems' pathways, and 'KEGG_disease' for 'Human Diseases' pathways. 'REACTOME' for protein-protein interactions derived from Reactome pathways

STRING.only

the further restriction of STRING by interaction type. If NA, no such restriction. Otherwide, it can be one or more of "neighborhood_score","fusion_score","cooccurence_score","coexpression_score","experimental_score","database_score","textmining_score". Useful options are c("experimental_score","database_score"): only experimental data (extracted from BIND, DIP, GRID, HPRD, IntAct, MINT, and PID) and curated data (extracted from Biocarta, BioCyc, GO, KEGG, and Reactome) are used

weighted

logical to indicate whether edge weights should be considered. By default, it sets to false. If true, it only works for the network from the STRING database

network.customised

an object of class "igraph". By default, it is NULL. It is designed to allow the user analysing their customised network data that are not listed in the above argument 'network'. This customisation (if provided) has the high priority over built-in network. If the user provides the "igraph" object with the "weight" edge attribute, RWR will assume to walk on the weighted network

seeds.inclusive

logical to indicate whether non-network seed genes are included for prioritisation. If TRUE (by default), these genes will be added to the netowrk

normalise

the way to normalise the adjacency matrix of the input graph. It can be 'laplacian' for laplacian normalisation, 'row' for row-wise normalisation, 'column' for column-wise normalisation, or 'none'

restart

the restart probability used for Random Walk with Restart (RWR). The restart probability takes the value from 0 to 1, controlling the range from the starting nodes/seeds that the walker will explore. The higher the value, the more likely the walker is to visit the nodes centered on the starting nodes. At the extreme when the restart probability is zero, the walker moves freely to the neighbors at each step without restarting from seeds, i.e., following a random walk (RW)

normalise.affinity.matrix

the way to normalise the output affinity matrix. It can be 'none' for no normalisation, 'quantile' for quantile normalisation to ensure that columns (if multiple) of the output affinity matrix have the same quantiles

parallel

logical to indicate whether parallel computation with multicores is used. By default, it sets to true, but not necessarily does so. Partly because parallel backends available will be system-specific (now only Linux or Mac OS). Also, it will depend on whether these two packages "foreach" and "doMC" have been installed

multicores

an integer to specify how many cores will be registered as the multicore parallel backend to the 'foreach' package. If NULL, it will use a half of cores available in a user's computer. This option only works when parallel computation is enabled

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

verbose.details

logical to indicate whether the detailed messages from being-called functions will be displayed in the screen. By default, it sets to FALSE enabling messages

RData.location

the characters to tell the location of built-in RData files. See xRDataLoader for details

guid

a valid (5-character) Global Unique IDentifier for an OSF project. See xRDataLoader for details

Value

A list of class "pNode" objects, each object having a list with following components:

Note

This function calls xPierSNPs in a loop way generating the distance predictor, the eQTL predictors (if required) and the HiC predictors (if required).

See Also

xPierSNPs

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
# a) provide the SNPs with the significance info
data(ImmunoBase)
gr <- ImmunoBase$AS$variants
AS <- as.data.frame(GenomicRanges::mcols(gr)[, c('Variant','Pvalue')])

# b) perform priority analysis
ls_pNode <- xPierSNPsAdv(data=AS, include.TAD='GM12878',
include.eQTL="JKng_mono", include.HiC='Monocytes',
network="PCommonsUN_medium", restart=0.7,
RData.location=RData.location)
#ls_pNode <- xPierSNPsAdv(data=AS, include.TAD='GM12878', include.eQTL="JKng_mono", include.HiC='Monocytes', network="PCommonsUN_medium", restart=0.7, RData.location=RData.location, eQTL.customised='eQTL.customised.Artery.txt')

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.