download_illumina_manifest_file: Download an Illumina array manifest

In drmjc/lumidat: Methods for importing Illumina gene expression iDAT files

Description

Illumina array manifest files (current and archived) are hosted in [1,2], and exist in 2 formats: bgx (compressed) and txt (most commonly used). Given the exact name of the array, this will download either the bgx or txt formatted manifest file to dir.

Usage

  download_illumina_manifest_file(array.name,
    type = c("txt", "bgx"), dir = ".", verbose = FALSE)

Arguments

array.name	the exact array name, including capitalisation, as it appears in [1,2] or list_illumina_manifest_files.
type	one of “txt” or “bgx”
dir	the directory to download to. defaults to current working dir.
verbose	logical

Value

a character vector(1) of the path to the downloaded manifest file

manifest files

These are the current (2012-10-14) array manifest names:

HumanHT-12_V3_0_R2_11283641_A

HumanHT-12_V3_0_R3_11283641_A

HumanHT-12_V4_0_R1_15002873_B

HumanHT-12_V4_0_R2_15002873_B

HumanHT-12_V4_0_R2_15002873_B_WGDASL

HumanMI_V1_R2_XS0000122-MAP

HumanMI_V2_R0_XS0000124-MAP

HumanRef-8_V2_0_R4_11223162_A

HUMANREF-8_V3_0_R1_11282963_A_WGDASL

HumanRef-8_V3_0_R2_11282963_A

HumanRef-8_V3_0_R3_11282963_A

HumanWG-6_V2_0_R4_11223189_A

HumanWG-6_V3_0_R2_11282955_A

HumanWG-6_V3_0_R3_11282955_A

MouseMI_V1_R2_XS0000127-MAP

MouseMI_V2_R0_XS0000129-MAP

MouseRef-8_V1_1_R4_11234312_A

MouseRef-8_V2_0_R2_11278551_A

MouseRef-8_V2_0_R3_11278551_A

MouseWG-6_V1_1_R4_11234304_A

MouseWG-6_V2_0_R2_11278593_A

MouseWG-6_V2_0_R3_11278593_A

RatRef-12_V1_0_R5_11222119_A

For the archived ones, see list_illumina_manifest_files.

Author(s)

Mark Cowley, 2012-10-14

See Also

list_illumina_manifest_files

Examples

## Not run: 
download_illumina_manifest_file("HumanHT-12_V4_0_R2_15002873_B", "txt")

## End(Not run)

drmjc/lumidat documentation built on May 15, 2019, 2:23 p.m.