readCdfNbrOfCellsPerUnitGroup: Gets the number of cells (probes) that each group of each...

In affxparser: Affymetrix File Parsing SDK

Description

Gets the number of cells (probes) that each group of each unit in a CDF file.

Usage

readCdfNbrOfCellsPerUnitGroup(filename, units=NULL, verbose=0)

Arguments

filename	The filename of the CDF file.
units	An integer vector of unit indices specifying which units to be read. If NULL, all units are read.
verbose	An integer specifying the verbose level. If 0, the file is parsed quietly. The higher numbers, the more details.

Value

A named list of named integer vectors. The name of the list elements are unit names and the names of the integer vector are group names.

Author(s)

Henrik Bengtsson

Examples

##############################################################
if (require("AffymetrixDataTestFiles")) {            # START #
##############################################################

cdfFile <- findCdf("Mapping10K_Xba131")

groups <- readCdfNbrOfCellsPerUnitGroup(cdfFile)

# Number of units read
print(length(groups))
##   11564

# Details on two units
print(groups[56:57])
## $`SNP_A-1516438`
## SNP_A-1516438C SNP_A-1516438T SNP_A-1516438C SNP_A-1516438T
##             10             10             10             10
##
## $`SNP_A-1508602`
## SNP_A-1508602A SNP_A-1508602G SNP_A-1508602A SNP_A-1508602G
##             10             10             10             10


# Number of groups with different number of cells
print(table(unlist(groups)))
##    10    60
## 46240     4


# Number of cells per unit
nbrOfCellsPerUnit <- unlist(lapply(groups, FUN=sum))
print(table(nbrOfCellsPerUnit))
nbrOfCellsPerUnit
##    40    60
## 11560     4


# Number of groups per unit
nbrOfGroupsPerUnit <- unlist(lapply(groups, FUN=length))

# Details on a few units
print(nbrOfGroupsPerUnit[20:30])
## SNP_A-1512666 SNP_A-1512740 SNP_A-1512132 SNP_A-1516082 SNP_A-1511962
##             4             4             4             4             4
## SNP_A-1515637 SNP_A-1515878 SNP_A-1518789 SNP_A-1518296 SNP_A-1519701
##             4             4             4             4             4
## SNP_A-1511743
##             4

# Number of units for each unique number of groups
print(table(nbrOfGroupsPerUnit))
## nbrOfGroupsPerUnit
##     1     4
##     4 11560

x <- list()
for (size in unique(nbrOfGroupsPerUnit)) {
  subset <- groups[nbrOfGroupsPerUnit==size]
  t <- matrix(unlist(subset), nrow=size)
  colnames(t) <- names(subset)
  x[[as.character(size)]] <- t
  rm(subset, t)
}

# Check if there are any quartet units where the number
# of cells in Group 1 & 2 or Group 3 & 4 does not have
# the same number of cells.
# Group 1 & 2
print(sum(x[["4"]][1,]-x[["4"]][2,] != 0))
# 0

# Group 3 & 4
print(sum(x[["4"]][3,]-x[["4"]][4,] != 0))
# 0

##############################################################
}                                                     # STOP #
##############################################################

affxparser documentation built on Nov. 8, 2020, 7:26 p.m.