Description Usage Arguments Details Value See Also
This function creates a snpinfo object.
1 2 3 4 5 |
.snpNames |
The field of si where the SNP identifiers are found. Default is 'Name' |
.aggregateBy |
The field of si on which the results were aggregated. Default is 'gene'. For single snps which are intended only for single variant analyses, it is reccomended that they have a unique identifier in this field. |
.chr |
(optional) The field of si where the chromosome identifiers are found. See Details. |
.pos |
(optional) The field of si where the snp position identifiers are found. See Details. |
.ref |
(optional) The field of si where the reference allele for the snps is found. See Details. |
.alt |
(optional) The field of si where the alternate allele for the snps is found. See Details. |
.filterBy |
(optional) The (typically logical) field in si in which to keep in further analysis. See Details |
.filterFun |
(optional) a function to apply to multiple '.filterBy' fields via |
.otherCols |
(optional) other fields of si to propagate through. See Details. |
si |
a data frame containing the SNP information. Must contain fields given in '.snpNames' and '.aggregateBy'. |
It is HIGHLY recommended that .chr
, .pos
, .ref
, and .alt
be supplied. For
.chr
and .pos
are used for branching and output in subsequent
analysis. Useful for analysis where the X chromosome is handled differently
than other chromosomes.
ref
and alt
are used in calculating various SNP and subject
summary statistics in 'genotype' objects.
.filterBy
and .filterFun
are used to create filters, typically
at the meta-analysis stage (e.g., because they are intronic or common).
TRUE
indicates that the SNP should be kept. If .filterFun
is
specified Reduce
will be applied to the columns specified by
.filterBy
. Note Reduce
is called the result must be a logical
vector for each entry in si
. If .filterFun
produces
NA
's, these will be changed to FALSE
with a warning.
.otherCols
an object of class 'snpinfo'. This is a list typicaly used to feed into an analysis function.
An object of class 'snpinfo' is a list containing at least the following components:
data containing the SNP information
snpNames column name containing the names of SNPs
aggregateBy column name which results are to be aggregated
chrCol column name containing the chromosome a SNP is found at.
posCol column name containing the position in a chromosome a SNP is found at.
refCol column name containing the reference allele.
altCol column name containing the alternate allele.
It is important to note that return include
and exclude
are taken from data and not from the input parameters.
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