ASC: Identify DCGs (Differential Coexpressed Genes) based on...

Description Usage Arguments Details Value Author(s) References Examples

Description

A method to pick out DCGs from microarray data based on 'Average Specific Connection' (ASC) (Choi et al. 2005).

Usage

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ASC(exprs.1, exprs.2, link.method = c("qth", "rth", "percent")[1], cutoff)

Arguments

exprs.1

a data frame or matrix for condition A, with rows as variables (genes) and columns as samples.

exprs.2

a data frame or matrix for condition B, with rows as variables (genes) and columns as samples.

link.method

a character string indicating link filtration method, default is 'qth'.

cutoff

the cutoff of correlation-value, q-value or percent of links after link filtering. must be within [0,1].

Details

ASC is the average value of the specific degree of the two conditions.

Value

ASC

the Average Specific Connections of genes. This measure can be used to rank gene in terms of differential coexpression.

Author(s)

Bao-Hong Liu, Hui Yu

References

Choi, J.K., Yu, U., Yoo, O.J. and Kim, S. (2005) Differential coexpression analysis using microarray data and its application to human cancer, Bioinformatics, 21, 4348-4355.

Examples

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data(exprs)
ASC(exprs[1:100,1:16],exprs[1:100,17:63],
	link.method = 'qth', cutoff=0.25)

Example output

    AACS    FSTL1    ELMO2  CREB3L1    RPS11    PNMA1     MMP2   SAMD4A 
    20.5     24.5     20.5     23.5     33.5     31.5     22.0     29.5 
 SMARCD3    A4GNT   PKNOX2    RALYL     ZHX3    ERCC5    GPR98    RXFP3 
    12.0     17.0     28.0     17.5     22.0     27.5     10.5     25.5 
   APBB2    BBOX1  PRO0478      XDH     EDN1    MTERF      AEN     CLK4 
    26.0     19.0     18.0     18.0     15.5     17.5     14.5     24.5 
   KCNG1    CXCR4    DECR1    SALL1    PTPRR    CADM4    IRAK1    CFHR5 
    25.0     19.0     18.5     22.5     16.5     17.0     25.0     17.5 
  TMSB10    CXCL3    LMAN1     CHD8    SUMO1    GP1BA   OR7A10     DDB1 
    28.5      7.5     17.5     17.5     24.0     21.5     21.5     25.0 
 CHRNA10    STYK1    MYO9B     CCNI     MMP7    EP300   CRNKL1  C9orf45 
    20.5     13.5     20.0     15.0     15.0     17.5     27.5     22.5 
    XAB2     RTN1     HIC2    TBX10    CENPQ      UTY    OR2W1    KCNA6 
    17.5     19.0     18.0     25.5     20.0      9.5     27.0     28.5 
  ATP5G2     ZEB1      ERG     FAT4     PARN     SOD2    CYTH1   ADAM5P 
    20.5     27.0     14.0     25.5     20.0     14.5     21.5     28.5 
    CHD9    STK16    PDE1C   SEMA4D   AGPAT1     TOB2    BANK1   MAP3K3 
    24.0     11.5     23.0     14.5     14.0     10.0     14.5     24.0 
     MAX     GRM2   OSBPL8    PROSC    NR4A2     RICS      PIR     PPCS 
     7.5     28.5     30.0     20.5     10.5     15.0     19.5     24.0 
    IPO9    LONP1      EVC   CXCL13    FFAR3    SCYL3 KIAA1199    SORL1 
    15.5     17.5     23.5     22.0     13.5     22.5     20.0     19.5 
   NAT10     CHD1     SYN3     DMC1  SLC22A2 SERPINF1 C20orf27   OR7A17 
    23.5     20.0     26.0     26.0     23.5     16.0     23.5     19.0 
 RPS6KA5     HMX1   DHRS11      LHB 
    10.5     20.5     16.5     11.5 

DCGL documentation built on May 1, 2019, 8:38 p.m.