chopsticks (version 1.36.0)

read.wtccc.signals: 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

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.

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)

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)