xGRscores: Function to score genomic regions based on the given...

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

xGRscores is supposed to score a list of genomic regions together with the significance level.

Usage

xGRscores(data, significance.threshold = 0.05, score.cap = 10, verbose
= T)

Arguments

data	a named input vector containing the sinificance level for genomic regions (GR). For this named vector, the element names are GR, in the format of 'chrN:start-end', where N is either 1-22 or X, start (or end) is genomic positional number; for example, 'chr1:13-20'. 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 GR, 2nd column for the significance level.
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 GR into scores. If given, those GR 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
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

a data frame with following columns:

• GR: genomic regions

• Score: the scores for GR calculated based on p-values taking into account the given threshold of the significant level

• Pval: the input p-values for GR

Note

None

See Also

xRDataLoader

Examples

## Not run: 
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

# a) provide the seed SNPs with the significance info
## load ImmunoBase
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
RData.location=RData.location)
## get lead SNPs reported in AS GWAS and their significance info (p-values)
gr <- ImmunoBase$AS$variant
df <- as.data.frame(gr, row.names=NULL)
chr <- df$seqnames
start <- df$start
end <- df$end
sig <- df$Pvalue
GR <- paste(chr,':',start,'-',end, sep='')
data <- cbind(GR=GR, Sig=sig)

# b) calculate GR scores (considering significant cutoff 5e-5)
df_GR <- xGRscores(data=data, significance.threshold=5e-5)

## End(Not run)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.