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Calculates binding enrichment for motif(s)

Source: R/enrichSEMs.R
enrichSEMs.Rd

Perform a binomial test to determine if SNP Effect Matrices are bound more often than expected.

Usage

enrichSEMs(x, sem, background = NULL, seqs = NULL, nFlank = 0, genome = NULL)

Arguments

x

The scoring table produced by scoreBinding

sem

A SNPEffectMatrix or SNPEffectMatrixCollection object

background

A GRanges object or a list of DNA sequences to use as a background set for the binomial test. The length of each sequence must match the length of sequences in x. By default, will scramble the provided sequences.

seqs

The sequences scored in scoreBinding

nFlank

Number of flanking nucleotides added to the sequences. Defaults to the length of the longest motif. If no flanks were added (ie, sequences were scored rather than a GRanges), use nFlank = 0.

genome

A BSGenome object. Requried if background isn't specified.

Value

a list of matrices

Details

In instances where scores for both forward and reverse orientations are provided, only the orientation with the highest binding score is considered for each sequence/SEM combination in enrichment calculations.

Examples


# load SEMs

# note that this is a small example for demonstration purposes
# in actual enrichment analyses sets of 100+ ranges are recommended

# create a GRanges object
gr <- GenomicRanges::GRanges(
    seqnames = "chr12",
    ranges = 94136009
)

# calculate binding propensity
sb <- scoreBinding(gr, SEMC, BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

enrichSEMs(sb, SEMC)
#> Building background set (this may take several minutes) ...
#>         SEM pvalue  padj n_bound n_bound_bg
#>      <char>  <num> <num>   <int>      <int>
#>   1: TFAP2B      1     1       0          0
#>   2:   ARNT      1     1       0          0
#>   3:   ATF1      1     1       0          0
#>   4:   ATF2      1     1       0          0
#>   5:   ATF3      1     1       0          0
#>  ---                                       
#> 219: ZBTB7A      1     1       0          0
#> 220:    ZFX      1     1       0          0
#> 221: ZNF281      1     1       0          0
#> 222:  ZNF18      1     1       0          0
#> 223: ZSCAN4      1     1       0          0