get_features: Load histone mark features, predictors

In seandavi/ProjectAsPkg: Just an example package

Description

This is a helper function that simply loads the the histone marks, one row per gene. Marks are given as column names. Row names are some strange mix of Ensembl IDs and junk.

Usage

get_features()

Value

a data.frame with histone marks in columns and one row per gene. Gene names are row names.

References

http://starbuck1.s3.amazonaws.com/expression-prediction/features.txt

Examples

feat = get_features()
head(feat)
# Do some multidimensional scaling
mds = cmdscale(dist(t(as.matrix(feat))))
plot(mds, type='n')
text(mds, labels=rownames(mds))
# limit to top 500 most variable "genes"
sds = apply(feat, 1, sd)
feat_500 = feat[order(sds, decreasing=TRUE)[1:500], ]
heatmap(as.matrix(feat_500))

seandavi/ProjectAsPkg documentation built on May 28, 2019, 11:06 a.m.