plot_HOMERTFs {HodgesTools}

Plot HOMER TF enrichment results

Description

Plot HOMER TF enrichment results

Usage

plot_HOMERTFs(
  dir = "/directory/of/results/",
  show = 3,
  qThreshold = 0.05,
  levenSimThreshold = 1
)

Arguments

dir

string. Input directory containing HOMER findMotifsGenome.pl output files in format: *knownResults.txt

show

int. Number of rows to show per input file, ranked by p-value.

qThreshold

int. Value for thresholding HOMER enrichment results by q-value.

levenSimThreshold

float. Value for thresholding TFs. For groups of TFs with similar consensus sequences, the TF with the lowest p-value by HOMER will be retained.

Details

Make bigTable of all TFs to pull from so a single TF can have data from different input Files (e.g. across CTs)

(5) Create bigTable of all q-value TF results concatenated together (6) Filter by consensus list (4)and make a gg-plot appropriate table and Plot (7-8) Order factors and plot

Value

ggplot object

Strategy:

Find motifs to extract

(1) Filter each element table by q-value. Should basically chop off the bottom portion of list, making the rest of the script less computationally cumbersome (2) Collapse each element table by by Levenshtein Similarity (3) Filter each element table (in my case: cell type-specific results file) to top X rows (4) Extract consensus columns from each element table and store as a variable]

Author(s)

Tim Scott