View source: R/genomic_matrix.R
ldscore | R Documentation |
This function calculates LD scores for the specified chromosome(s) based on genotypic data provided in 'Glist'. The LD score quantifies the amount of Linkage Disequilibrium at a given SNP.
ldscore(
Glist = NULL,
chr = NULL,
onebased = TRUE,
nbytes = 4,
cm = NULL,
kb = NULL
)
Glist |
A list structure with genotypic data stored, including positions ('pos'), map information ('map'), rsids for LD calculation ('rsidsLD'), and LD file locations ('ldfiles'). |
chr |
A single chromosome or a vector of chromosomes for which LD scores need to be computed. Default is NULL, implying all chromosomes in 'Glist' will be used. |
onebased |
Logical, if 'TRUE', the indexing of positions and other genomic information is 1-based. Default is 'TRUE'. |
nbytes |
The size (in bytes) of each numeric value to read from the binary LD files. Default is 4. |
cm |
The threshold in centiMorgans for filtering LD values. Default is NULL. |
kb |
The threshold in kilobases for filtering LD values. Default is NULL. If specified, it will be converted to base pairs internally. |
The function computes the LD scores for each SNP by reading LD values from binary files stored in 'Glist$ldfiles'. It can filter SNPs based on physical distance ('kb') or genetic map distance ('cm'). If both 'cm' and 'kb' are NULL, all LD values are used in computation.
A list containing computed LD scores for each chromosome in the input.
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