Import a deepTools Matrix File as a SummarizedExperiment Object

importDeeptoolsExperiment(file, col.names = NULL)

Arguments

file	A gzip-compressed matrix file.
col.names	A character vector of column names immediately set on the output object.

Value

A SummarizedExperiment object. See Details.

Details

Matrix files produced by deepTools do not include column names that are useful to indicate the genomic position relative to a reference point, for instance. While colnames could be manually set by users on the SummarizedExperiment returned, it can be convenient to provide a set of column names directly to the importDeeptoolsExperiment() function, especially when importing multiple samples in an lapply() statement, for instance.

The returned object contains:

The deepTools matrix in the assay slot.
The genomic range information in the rowRanges slot.

Examples

library(rtracklayer)
library(GenomicRanges)

# Prepare example data ----

se_list <- generateDeeptoolsExperiments(ranges=20, bins=10, names=c("A"))
se_list
#> $A
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 

# Write example file ----

se_A <- se_list[["A"]]
gr_A <- rowRanges(se_A)
df_A <- data.frame(
  seqnames(gr_A), start(gr_A), end(gr_A), names(gr_A), 0, strand(gr_A),
  assay(se_A))

# Write the sample data to file
tf <- tempfile(fileext=".matrix.gz")
conn <- gzfile(tf, "wt")
write.table(df_A, conn, row.names=FALSE, col.names=TRUE)
close(conn)

# Usage ----

importDeeptoolsExperiment(tf)
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):