Motif Analysis in Signac Species ID ?

[coopershawna]

Quick question... for the motif analysis of mouse tissue... the taxonomy ID 9606 is human and is the same one used in the human transcription factor footprinting vignette... Should it be switched to the mouse id of 10090 or is there a very good reason for using the human one?

Thank you!

mouse motif analysis vignette

# Get a list of motif position frequency matrices from the JASPAR database
pfm <- getMatrixSet(
  x = JASPAR2020,
  opts = list(species = **9606,** all_versions = FALSE)
)

# add motif information
mouse_brain <- AddMotifs(
  object = mouse_brain,
  genome = BSgenome.Mmusculus.UCSC.mm10,
  pfm = pfm
)

# extract position frequency matrices for the motifs    Human TF vignette
pwm <- getMatrixSet(
  x = JASPAR2018,
  opts = list(species = **9606**, all_versions = FALSE)
)

# add motif information
bone <- AddMotifs(bone, genome = BSgenome.Hsapiens.UCSC.hg19, pfm = pwm)

[timoast]

Please see #58

[coopershawna]

Thank you! I appreciate your help and prompt replies!!!!