| Title: | Illumina 450k data on sorted cord blood cells |
|---|---|
| Description: | Raw data objects to be used for cord blood cell proportion estimation in minfi. |
| Authors: | Shan V. Andrews [cre, aut], Kelly M. Bakulski [aut] |
| Maintainer: | Shan V. Andrews <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.40.0 |
| Built: | 2026-10-10 11:27:03 UTC |
| Source: | https://git.bioconductor.org/packages/FlowSorted.CordBlood.450k |
This RGChannelSet contains Illumina 450k measurements on 17 cord blood samples, each of
which contribute between 4 and 7 sorted cell populations. These 7 cell populations are:
B cells, CD4 T cells, CD8 T cells, granulocytes, monocytes, natural killer cells, and
nucleated red blood cells.
data(FlowSorted.CordBlood.450k)data(FlowSorted.CordBlood.450k)
Please see manuscript for additional details on cord blood samples and prediction pipeline.
An RGChannelSet.
Bakulski KM, Feinberg JI, Yang J, Brown S, Andrews SV, McKenney S, Witter F, Walston J, Feinberg AP, Fallin MD. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Epigenetics (2016), 11:354-362. doi:10.1080/15592294.2016.1161875.
data(FlowSorted.CordBlood.450k)data(FlowSorted.CordBlood.450k)
Association of probes on the 450k with cord blood cell composition. Please see manuscript for probe filtering criteria.
data(FlowSorted.CordBlood.450k.compTable)data(FlowSorted.CordBlood.450k.compTable)
A data frame with 429794 observations on the following 12 variables.
Fstatf-statistic for composition from ANOVA. See estimateCellCounts in minfi.
p.valuep-value corresponding to f-statistic.
Bcellmean methylation level across 15 B cell replicates.
CD4Tmean methylation level across 15 CD4 T-cell replicates.
CD8Tmean methylation level across 14 CD8 T-cell replicates.
Granmean methylation level across 12 granulocyte replicates.
Monomean methylation level across 15 monocyte replicates.
NKmean methylation level across 14 natural killer cell replicates.
nRBCmean methylation level across 4 nucleated red blood cell replicates.
lowlow value of methylation across all samples.
highhigh value of methylation across all samples.
rangerange of methylation values across all samples.
Our recommedations for this object parallel those given in the (adult) blood companion package, FlowSorted.Blood.450k. Briefly, this object can be used to evaluate the potetial for cofounding by cell-type heterogeneity at 450k probes following an associaton study.
A data frame with 429794 observations and 12 variables.
Bakulski KM, Feinberg JI, Yang J, Brown S, Andrews SV, McKenney S, Witter F, Walston J, Feinberg AP, Fallin MD. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Manuscript in review.
data(FlowSorted.CordBlood.450k.compTable)data(FlowSorted.CordBlood.450k.compTable)
This object is generated during the course of cord blood cell proportion estimation in the minfi estimateCellCounts function.
data(FlowSorted.CordBlood.450k.ModelPars)data(FlowSorted.CordBlood.450k.ModelPars)
A matrix of 700 rows and 7 columns, the latter corresponding to
7 cell types. 100 probes were selected as being differentially methylated
by each cell type from the reference RGset contained herein (FlowSorted.CordBlood.450k).
In the implementation of the estimateCellCounts function,
probes are selected based on a combined RGset of user and reference data.
Please see manuscript for details on the probe selection process.
A matrix with 700 rows and 7 columns.
Bakulski KM, Feinberg JI, Yang J, Brown S, Andrews SV, McKenney S, Witter F, Walston J, Feinberg AP, Fallin MD. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Manuscript in review.
data(FlowSorted.CordBlood.450k.ModelPars)data(FlowSorted.CordBlood.450k.ModelPars)