xGRscores | R Documentation

## Function to score genomic regions based on the given significance level

### 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, RData.location = "http://galahad.well.ox.ac.uk/bigdata")

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

### 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,
    RData.location=RData.location)

    ## End(Not run)