Description Arguments Details Value Author(s) References See Also Examples
DMarker
is a package to predict whether the protein or gene can be detected in blood and urine.
The fuction dmarker
is the main function of the package. It predicts the biomarker in a data vector, and helps to know whether the protein or gene can be detected in blood and urine.
results = dmarker(data, ...);
data |
Data vector. |
pre |
-pre should be ( "gene", "protein" ), is a data type variable, telling DMarker gene or protein you are using. |
file |
-file should be a filename to output the results if want to save that, or use "FALSE" to ignore. |
type |
-type should be ( "both", "blood", "urine" ), is a predict type variable, telling DMarker where the data can be detected in blood, urine or both. |
Seq |
-Seq should be ( "T", "F" ). If Seq is True, the DMarker would predic the sequence whether can be detect in blood or urine, and the data vector must be the sequence vector. |
results = dmarker(data, pre = "Gene", file = "FALSE", type = "both");
The R function, dmarker
returns an object of list
:
BLOOD | An object of list , having GENE and PROTEIN . |
URINE | An object of list , having GENE and PROTEIN . |
GENE | A result vector, containing the gene names which can be detected in BLOOD or URINE . |
PROTEIN | A result vector, containing the protein names which can be detected in BLOOD or URINE . |
The R function, dmarker
will write the results in a file named by -file, if -file is not FALSE by default. The file will be in the Working Directory
.
Yu Shang (JLU & UGA) yushang@uga.edu
Qiong Yu (JLU & UGA) yuqiong@uga.edu
Wei Du (JLU & UGA) weidu@uga.edu
Ying Xu (JLU & UGA) xyn@bmb.uga.edu
Maintainer: Yu Shang (JLU & UGA) yushang@uga.edu
[1]
Yan Wang, et al. (2009) DMarker: A Bio-Marker Inference System for Human Diseases based
on Microarray Gene Expression Data 2009
[2]
Juan Cui, et al. (2008) Computational prediction of human proteins that can be secreted into the bloodstream BIOINFORMATICS, Vol.24 no. 20 2008 pages 2370-2375
[3]
Jiaxin Wang, et al. (2013) Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification PLoS ONE, DOI: 10.1371/journal.pone.0080211, 2013
[4]
S Hong, et al. (2011) A Computational Method for Prediction of Excretory Proteins and Application to Identification of cancer markers in urine and application to gastric cancer PLoS ONE,6(2):e16875, 2011
[5]
http://bioinfosrv1.bmb.uga.edu/DMarker/
DMarker-package
DMarker-method
uniprot
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | data(data);
# load the example vector
results = dmarker(data);
# run dmarker with default parameters
# results is a variable of list with,
# $BLOOD,
# $BLOOD$GENE, which genes can be detected in BLOOD,
# $BLOOD$PROTEIN, which proteins can be detected in BLOOD,
# $URINE,
# $URINE$GENE, which genes can be detected in BLOOD,
# $URINE$PROTEIN, which proteins can be detected in URINE,
# or results = dmarker(data, pre = "Gene", file = "FALSE", type = "both");
results = dmarker(data, pre = "Gene", file = "DMarkerResults.txt", type = "both", Seq = "F");
# Saving the results both in R variable results and the file named DMarkerResults.txt by -file.
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