read.wtccc.signals {chopsticks} | R Documentation

## read normalized signals in the WTCCC signal file format

### Description

`read.wtccc.signals` takes a file and a list of snp ids (either Affymetrix ProbeSet IDs or rs numbers), and extract the entries into a form suitable for plotting and further analysis

### Usage

    read.wtccc.signals(file, snp.list)

### Arguments

`file` | `file` contains the signals. There is no need to gunzip.
`snp.list` | A list of snp id's. Some Affymetrix SNPs don't have rsnumbers both rsnumbers and Affymetrix ProbeSet IDs are accepted

### Details

Do not specify both rs number and Affymetrix Probe Set ID in the input; one of them is enough.

The signal file is formatted as follows, with the first 5 columns being the Affymetrix Probe Set ID, rs number, chromosome position, AlleleA and AlleleB. The rest of the header containing the sample id appended with "\_A" and "\_B".

      AFFYID         RSID       pos   AlleleA AlleleB 12999A2_A 12999A2_B ...
      SNP_A-4295769  rs915677   14433758  C     T     0.318183  0.002809
      SNP_A-1781681  rs9617528  14441016  A     G     1.540461  0.468571
      SNP_A-1928576  rs11705026 14490036  G     T     0.179653  2.261650

The routine matches the input list against the first and the 2nd column.

(some early signal files, have the first "AFFYID" missing - this routine can cope with that also)

### Value

The routine returns a list of named matrices, one for each input SNP (`NULL` if the SNP is not found); the row names are sample IDs and columns are "A", "B" signals.

### Note

TODO: There is a built-in limit to the input line buffer (65535) which should be sufficient for 2000 samples and 30 characters each. May want to seek backwards, re-read and dynamically expand if the buffer is too small.

### Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

### References

http://www.wtccc.org.uk

### Examples

    ## Not run:
    answer <-
      read.wtccc.signals("NBS_22_signals.txt.gz", c("SNP_A-4284341","rs4239845"))
    > summary(answer)
                  Length Class  Mode
    SNP_A-4284341 2970   -none- numeric
    rs4239845     2970   -none- numeric

    > head(a$"SNP_A-4284341")
                   A        B
    12999A2 1.446261 0.831480
    12999A3 1.500956 0.551987
    12999A4 1.283652 0.722847
    12999A5 1.549140 0.604957
    12999A6 1.213645 0.966151
    12999A8 1.439892 0.509547
    >

    ## End(Not run)

[Package chopsticks version 1.54.0 Index]