dataSimExample {methInheritSim} | R Documentation |
list
containing methylation information used by some internal
functions (for demo purpose.A list
containing methylation information used by some internal
functions (for demo purpose.
data(dataSimExample)
a list
containing:
stateInfo
a GRanges
, a synthetic chromosome as
generated by getSyntheticChr
function.
stateDiff
a list
containing:
stateDiff
a vector
of integer
(0
and 1
) with length corresponding the length of stateInfo
.
The vector
indicates, using 1
, the positions where the CpG sites are
differentially methylated.
stateInherite
a vector
of integer
(0
and
1
) with length corresponding the length of stateInfo
. The
vector
indicates, using 1
, the positions where the CpG values are
inherited.
treatment
a vector
of integer
(0
and 1
) with length corresponding the number of samples. The
vector
indicates which samples are control (0) which samples are
case (1).
sample.id
a list
of 3 list
. Each entry of the
list
correspond to one generation (first entry = first generation,
etc..). Each
list
contains a list
of 12 entries each containing a string
of character
, the name of the sample.
a list
containing:
stateInfo
a GRanges
, a synthetic chromosome as
generated by getSyntheticChr
function.
stateDiff
a list
containing:
stateDiff
a vector
of integer
(0
and 1
) with length corresponding the length of stateInfo
.
The vector
indicates, using 1
, the positions where the CpG sites are
differentially methylated.
stateInherite
a vector
of integer
(0
and
1
)
with length corresponding the length of stateInfo
. The
vector
indicates, using 1
, the positions where the CpG values are
inherited.
treatment
a vector
of integer
(0
and 1
) with length corresponding the number of samples. The
vector
indicates which samples are control (0) which samples are
case (1).
sample.id
a list
of 3 list
. Each entry of the
list
correspond to one generation (first entry = first generation,
etc..). Each
list
contains a list
of 12 entries each containing a string
of character
, the name of the sample.
runSim
for running a
simulation analysis using methylKit info as input
## Loading dataset data(dataSimExample) ## Identify differentially methylated sites and among those, the ones ## that are inherited methInheritSim:::getDiffMeth(stateInfo = dataSimExample$stateInfo, rateDiff = 0.2, minRate = 0.3,propInherite = 0.3)