synergise
function of the synapter
package and combines resulting
Synapter
instances into one "MSnSet"
and organelle marker data is added as a feature-level annotation variable.
lopims(hdmsedir = "HDMSE", msedir = "MSE", pep3ddir = "pep3D", fastafile, markerfile, mfdr = 0.025, ...)
character
identifying the directory
containing the HDMSe final peptide files. Default is HDMSe
.character
identifying the directory
containing the MSe final peptide files. Default is MSe
.character
identifying the directory
containing the MSe pep 3D files. Default is pep3D
.character
identifying the protein
fasta database. Default is to use the fasta file in the current
directory. If several such files exist, the function reports an
error.character
identifying the marker
file (see details for format). Default is to use a csv
file
starting with marker
in the current directory.
If several such files exist, the function reports an error.synergise
."MSnSet"
with protein
level quantitation and respective organelle markers.
LOPIMS
pipeline is composed of 5 steps:mfdr
is chosen. See
estimateMasterFdr
for details. The
corresponding master run is then created as descibed in
makeMaster
. (function lopims1
)
synergise
. (function lopims2
)
synergise
output objects
are converted and combined into an single
"MSnSet"
instance. (function lopims3
)
NA
). If several samples have a same
minimal number of NA
s, ties are broken using the sum of
counts. The peptides that do not display any missing values for
each (frac_i, frac_ref) pair are summed and the ratio is
reported (see pRoloc:::refNormMeanOfNonNAPepSum for
details). (function lopims4
)
markerfile
are collated as
feature meta-data in the markers
variable. See
addMarkers
for details. (function lopims5
)
Intermediate synergise
reports as well as resulting objects
are stored in a LOPIMS_pipeline
directory.
For details, please refer to the synapter
vignette and
reference papers.
The Effects of Travelling Wave Ion Mobility Separation on Data Independent Acquisition in Proteomics Studies P.V. Shliaha, N.J. Bond, L. Gatto and K.S. Lilley Journal of Proteome Research, 2013;12(6):2323-39. PMID: 23514362.
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. L. Gatto and KS. Lilley. Bioinformatics. 2012 Jan 15;28(2):288-9. doi: 10.1093/bioinformatics/btr645. Epub 2011 Nov 22. PubMed PMID: 22113085.