tests/testthat.R

In mengchen18/PTMotif: Detect PTM motifs

library(testthat)
library(PTMotif)

data("motifExampleData")
a <- motifExampleData

# checkSeqs
checkSeqs(fg.seqs = a$foreground[1:2], bg.seqs = a$foreground[1:3])
checkSeqs(fg.seqs = c(a$foreground[1:2], "LFLPPSKTVLPTVPEQPEEEVKASQLSVQQN"), 
          bg.seqs = a$foreground[1:3])
checkSeqs(fg.seqs = c(a$foreground[1:2], "LFLPPSKTVLPTVPEQPEEEVKASQLSVQQN"), 
          bg.seqs = a$foreground[1:3], center = NULL)
checkSeqs(fg.seqs = a$foreground[1:2], bg.seqs = a$foreground[1:3], center = NULL)


# motif_all

seq <- c("ALNQKTSEKMKKRKMSNSFHGIRPPQLEQPE", 
         "REHSYVLSAAKKSTGSPTQETQAPFIAKRVE",
         "SSKKMGSIFDREDQASPRAGSLAALEKRQAE",
         "GELYDKSIIQSAQQDSIKKANMKRENKAYSF",
         "VHRDLKPENILYADDTPGAPVKIIDFGFARL",
         "MSLSAGSSPLHSPKITPHTSPAPRRRSHTPN")

v <- motif_all(seq, min.seqs = 2)
v0 <- motif_all(seq, min.seqs = 2, center = NULL)
all(names(v$mw) %in% names(v0$mw))
all(names(v0$mw) %in% names(v$mw))

length(v0$mw)
length(v$mw)

seq <- c("ALNQKTSEKMKKSTMSNSFHGIRPP______", 
         "REHSYVLSAAKKSTGSPTQETQAPF______",
         "SSKKMGSIFDRESTASPRAGSLAAL______",
         "GELYDKSIIQSASTDSIKKANMKRE______",
         "VHRDLKPENILYSTDTPGAPVKIID______",
         "MSLSAGSSPLHSPKITPHTSPAPRR______")

v <- motif_all(seq, min.seqs = 5)
v <- motif_all(seqs = a$background[1:10], min.seqs = 3)



# detectMotifs
v <- detectMotifs(a$background[1:10], a$background[1:100], min.seqs = 3, method = "all", ncores = 1)
v <- detectMotifs(a$background[1:3], a$background[1:100], min.seqs = 5, method = "all", ncores = 1)
v <- detectMotifs(a$background[1:10], a$background[1:11], min.seqs = 5, method = "all", ncores = 1)
v <- detectMotifs(a$background[1:5], a$background[1:5], min.seqs = 5, method = "all", ncores = 1)


v1 <- detectMotifs(
  a$background[1:10], a$background[1:100], 
  fg.genes = paste0("g", 1:10), bg.genes = paste0("g", 1:100), 
  min.seqs = 3, method = "all", ncores = 1, max.pvalue = 0.5
)

v2 <- detectMotifs(
  a$background[1:10], a$background[1:100], 
  fg.genes = paste0("g", 1:10), bg.genes = paste0("g", 1:100), 
  min.seqs = 3, method = "cvp", ncores = 1, max.pvalue = 0.5
)

v3 <- detectMotifs(
  a$background[1:10], a$background[1:100], 
  fg.genes = paste0("g", 1:10), bg.genes = paste0("g", 1:100), 
  min.seqs = 3, method = c("all", "cvp"), ncores = 1, max.pvalue = 0.5
)

v4 <- detectMotifs(
  a$background[1:10], a$background[1:100], 
  fg.genes = paste0("g", rep(1, 10)), bg.genes = paste0("g", 1:100), 
  min.seqs = 3, method = c("all", "cvp"), ncores = 1, max.pvalue = 0.5
)


# v <- detectMotifs(
#   a$foreground, a$background, min.seqs = 3, method = "all", ncores = 1, max.pvalue = 0.5
# )