Description Usage Arguments Details Value See Also Examples

Cell-Type-Specific QTL analysis

1 2 3 4 5 6 7 8 9 10 11 |

`X` |
Matrix (or vector) of SNP genotypes; SNPs x samples. |

`Xpos` |
Vector of the physical position of X |

`W` |
Matrix of cell type composition; samples x cell types. |

`Y` |
Matrix (or vector) of bulk omics measurements; markers x samples. |

`Ypos` |
Vector of the physical position of Y |

`C` |
Matrix (or vector) of covariates; samples x covariates. X, Xpos, W, Y, Ypos, C should be numeric. |

`max.pos.diff` |
Maximum positional difference to compute cis-QTL. Association analysis is performed between a row of X and a row of Y, only when they are within this limit. Since the limiting is only by position, the function needs to be run separately for each chromosome. |

`outdir` |
Output directory. |

`outfile` |
Output file. |

A function for analyses of QTL, such as eQTL, mQTL, pQTL.
The statistical test is almost identical to
`ctassoc(test = "nls.identity", regularize = "TRUE")`

.
Association analysis is performed between each row of Y and each row of X.
Usually, the former will be a methylation/expression marker,
and the latter will be a SNP.
To cope with the large number of combinations,
the testing is limited to pairs whose position is within
the difference specified by `max.pos.diff`

; i.e., limited to cis-QTL.
In detail, this function performs linear ridge regression,
whereas `ctassoc(test = "nls.identity", regularize = "TRUE")`

actually is nonlinear regression
but with *f* = identity as normalizing transformation.
In order to speed up computation, first, the parameters *α_{h j}* and
*γ_{j l}* are fit by ordinary linear regression assuming *β_{h j k} = 0*.
Next, *β_{h j k}* are fit and tested by
linear ridge regression (see documentation for ctassoc).

The estimate, statistic, p.value are written to the specified file.

ctassoc

1 2 3 4 5 6 7 8 9 10 | ```
data(GSE79262small)
X = GSE79262small$X
Xpos = GSE79262small$Xpos
W = GSE79262small$W
Y = GSE79262small$Y
Ypos = GSE79262small$Ypos
C = GSE79262small$C
X = X[seq(1, 3601, 100), ] # for brevity
Xpos = Xpos[seq(1, 3601, 100)]
ctcisQTL(X, Xpos, W, Y, Ypos, C = C)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.