dmarker: DMarker main function
In yu-shang/DMarker: DMarker

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. default: "GENE"
`file`	-file should be a filename to output the results if want to save that, or use "FALSE" to ignore. default: "FALSE"
`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. default: "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. default: "F"

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

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.