R/ENCODE.R
downloadENCODEknockdownMetadata.RdDownload metadata for ENCODE knockdown experiments
downloadENCODEknockdownMetadata(
cellLine = NULL,
gene = NULL,
file = "ENCODEmetadata.rds"
)Character: cell line
Character: target gene
Character: RDS filepath with metadata (if file doesn't exist, it will be created)
Data frame containing ENCODE knockdown experiment metadata
Other functions related with using ENCODE expression data:
loadENCODEsamples(),
performDifferentialExpression(),
prepareENCODEgeneExpression()
downloadENCODEknockdownMetadata("HepG2", "EIF4G1")
#> Downloading metadata for ENCODE knockdown experiments...
#> File accession File format File type File format type Output type
#> <char> <char> <char> <char> <char>
#> 1: ENCFF955TXI tsv tsv gene quantifications
#> 2: ENCFF049UZV tsv tsv gene quantifications
#> File assembly Experiment accession Assay Donor(s)
#> <char> <char> <char> <char>
#> 1: hg19 ENCSR509LIV shRNA RNA-seq /human-donors/ENCDO000AAC/
#> 2: hg19 ENCSR509LIV shRNA RNA-seq /human-donors/ENCDO000AAC/
#> Biosample term id Biosample term name Biosample type Biosample organism
#> <char> <char> <char> <char>
#> 1: EFO:0001187 HepG2 cell line Homo sapiens
#> 2: EFO:0001187 HepG2 cell line Homo sapiens
#> Biosample treatments Biosample treatments amount
#> <lgcl> <lgcl>
#> 1: NA NA
#> 2: NA NA
#> Biosample treatments duration Biosample genetic modifications methods
#> <lgcl> <char>
#> 1: NA RNAi
#> 2: NA RNAi
#> Biosample genetic modifications categories
#> <char>
#> 1: interference
#> 2: interference
#> Biosample genetic modifications targets
#> <char>
#> 1: {'schema_version': '14', 'aliases': [], 'organism': {'schema_version': '6', '@type': ['Organism', 'Item'], 'name': 'human', 'taxon_id': '9606', 'scientific_name': 'Homo sapiens', '@id': '/organisms/human/', 'uuid': '7745b647-ff15-4ff3-9ced-b897d4e2983c', 'status': 'released'}, 'genes': ['/genes/1981/'], '@type': ['Target', 'Item'], 'name': 'EIF4G1-human', 'label': 'EIF4G1', '@id': '/targets/EIF4G1-human/', 'title': 'EIF4G1 (Homo sapiens)', 'investigated_as': ['RNA binding protein'], 'uuid': 'cc45c7a4-2d7a-4e86-9ca0-7429983a0aab', 'status': 'released'}
#> 2: {'schema_version': '14', 'aliases': [], 'organism': {'schema_version': '6', '@type': ['Organism', 'Item'], 'name': 'human', 'taxon_id': '9606', 'scientific_name': 'Homo sapiens', '@id': '/organisms/human/', 'uuid': '7745b647-ff15-4ff3-9ced-b897d4e2983c', 'status': 'released'}, 'genes': ['/genes/1981/'], '@type': ['Target', 'Item'], 'name': 'EIF4G1-human', 'label': 'EIF4G1', '@id': '/targets/EIF4G1-human/', 'title': 'EIF4G1 (Homo sapiens)', 'investigated_as': ['RNA binding protein'], 'uuid': 'cc45c7a4-2d7a-4e86-9ca0-7429983a0aab', 'status': 'released'}
#> Biosample genetic modifications gene targets
#> <lgcl>
#> 1: NA
#> 2: NA
#> Biosample genetic modifications site coordinates
#> <lgcl>
#> 1: NA
#> 2: NA
#> Biosample genetic modifications zygosity Experiment target
#> <lgcl> <char>
#> 1: NA EIF4G1
#> 2: NA EIF4G1
#> Library made from Library depleted in
#> <char> <char>
#> 1: polyadenylated mRNA
#> 2: polyadenylated mRNA
#> Library extraction method
#> <char>
#> 1: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
#> 2: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
#> Library lysis method Library crosslinking method Library strand specific
#> <lgcl> <lgcl> <char>
#> 1: NA NA reverse
#> 2: NA NA reverse
#> Experiment date released Project RBNS protein concentration
#> <IDat> <char> <lgcl>
#> 1: 2015-08-18 ENCODE NA
#> 2: 2015-08-18 ENCODE NA
#> Library fragmentation method Library size range Biological replicate(s)
#> <char> <char> <char>
#> 1: chemical (Illumina TruSeq) >200 1
#> 2: chemical (Illumina TruSeq) >200 2
#> Technical replicate(s) Read length Mapped read length Run type Paired end
#> <char> <int> <int> <char> <int>
#> 1: 1_1 NA NA NA
#> 2: 2_1 NA NA NA
#> Paired with Index of Derived from Size
#> <char> <lgcl> <char> <i64>
#> 1: NA /files/ENCFF995LZN/, /files/ENCFF826ONU/ 9554701
#> 2: NA /files/ENCFF447GOE/, /files/ENCFF826ONU/ 9563218
#> Lab md5sum dbxrefs
#> <char> <char> <char>
#> 1: ENCODE Processing Pipeline f9b46cbff89bfe91bdb0879b81cf41e8
#> 2: ENCODE Processing Pipeline 9f77694ffdf48801edb9c39f75f6d3b7
#> File download URL
#> <char>
#> 1: https://www.encodeproject.org/files/ENCFF955TXI/@@download/ENCFF955TXI.tsv
#> 2: https://www.encodeproject.org/files/ENCFF049UZV/@@download/ENCFF049UZV.tsv
#> Genome annotation Platform Controlled by File Status
#> <char> <char> <char> <char>
#> 1: V19 released
#> 2: V19 released
#> s3_uri
#> <char>
#> 1: s3://encode-public/2015/08/26/f02dd75d-a0c9-451f-aae8-23eb5e8a5a2f/ENCFF955TXI.tsv
#> 2: s3://encode-public/2015/08/26/d03e3680-479e-470b-9126-198e6cefe4dc/ENCFF049UZV.tsv
#> Azure URL
#> <char>
#> 1: https://datasetencode.blob.core.windows.net/dataset/2015/08/26/f02dd75d-a0c9-451f-aae8-23eb5e8a5a2f/ENCFF955TXI.tsv?sv=2019-10-10&si=prod&sr=c&sig=9qSQZo4ggrCNpybBExU8SypuUZV33igI11xw0P7rB3c%3D
#> 2: https://datasetencode.blob.core.windows.net/dataset/2015/08/26/d03e3680-479e-470b-9126-198e6cefe4dc/ENCFF049UZV.tsv?sv=2019-10-10&si=prod&sr=c&sig=9qSQZo4ggrCNpybBExU8SypuUZV33igI11xw0P7rB3c%3D
#> File analysis title File analysis status
#> <char> <char>
#> 1: Mixed pipelines hg19 V19 released
#> 2: Mixed pipelines hg19 V19 released
#> Audit WARNING Audit NOT_COMPLIANT Audit ERROR
#> <char> <char> <lgcl>
#> 1: missing biosample characterization NA
#> 2: missing biosample characterization NA
#> Control Control Experiments
#> <char> <char>
#> 1: ENCSR042QTH ENCFF657KMW, ENCFF726AVT
#> 2: ENCSR042QTH ENCFF657KMW, ENCFF726AVT