The MGI report MGI_MRK_Coord.rpt lists mouse genetic
markers along with their genomic annotations, such as chromosome
position, genome assembly version, and the source of the annotation.
To read this report using the key "marker_coordinates",
use the following code:
# To read all records (more than 600,000), use `read_report("marker_coordinates")`.
(marker_coord <- read_report(report_key = "marker_coordinates", n_max = 300L))## # A tibble: 300 × 12
## marker_type marker_id marker_symbol marker_name feature_type chromosome
## <fct> <chr> <chr> <chr> <fct> <fct>
## 1 Other Genome Fea… MGI:7712… Rr517 regulatory… enhancer 17
## 2 Gene MGI:87854 Pzp PZP, alpha… protein cod… 6
## 3 Gene MGI:87859 Abl1 c-abl onco… protein cod… 2
## 4 Gene MGI:87862 Scgb1b27 secretoglo… protein cod… 7
## 5 Gene MGI:87863 Scgb2b27 secretoglo… protein cod… 7
## 6 Gene MGI:87864 Scgb2b26 secretoglo… protein cod… 7
## 7 Gene MGI:87866 Acadl acyl-Coenz… protein cod… 1
## 8 Gene MGI:87867 Acadm acyl-Coenz… protein cod… 3
## 9 Gene MGI:87868 Acads acyl-Coenz… protein cod… 5
## 10 Gene MGI:87870 Acat1 acetyl-Coe… protein cod… 9
## # ℹ 290 more rows
## # ℹ 6 more variables: start <int>, end <int>, strand <fct>, assembly <fct>,
## # source <fct>, database <fct>For the first 300 records, here is the count by marker type:
dplyr::count(marker_coord, marker_type)## # A tibble: 4 × 2
## marker_type n
## <fct> <int>
## 1 Gene 36
## 2 Pseudogene 1
## 3 DNA Segment 261
## 4 Other Genome Feature 2By chromosome:
dplyr::count(marker_coord, chromosome)## # A tibble: 16 × 2
## chromosome n
## <fct> <int>
## 1 1 4
## 2 2 4
## 3 3 2
## 4 4 1
## 5 5 5
## 6 6 1
## 7 7 4
## 8 8 2
## 9 9 8
## 10 10 70
## 11 11 191
## 12 12 1
## 13 13 2
## 14 14 1
## 15 15 1
## 16 17 3By annotation source:
dplyr::count(marker_coord, source, database)## # A tibble: 5 × 3
## source database n
## <fct> <fct> <int>
## 1 NCBI NCBI Gene Model 19
## 2 Ensembl Ensembl Gene Model 18
## 3 MGI MGI 261
## 4 MGI NA 1
## 5 VISTA VISTA Gene Model 1Variables
marker_type
marker_type: genetic marker type is a factor of 10
levels: Gene, GeneModel, Pseudogene, DNA Segment, Transgene, QTL,
Cytogenetic Marker, BAC/YAC end, Complex/Cluster/Region, Other Genome
Feature. See ?marker_type_definitions for the meaning of
each type.
marker_id
marker_id: MGI accession identifier. A unique
alphanumeric character string that is used to unambiguously identify a
particular record in the Mouse Genome Informatics database. The format
is MGI:nnnnnn, where n is a digit.
marker_name
marker_name: marker name is a word or phrase that
uniquely identifies the genetic marker, e.g. a gene or allele name.
feature_type
feature_type: an attribute of a portion of a genomic
sequence. See the dataset ?feature_type_definitions for
details.
chromosome
chromosome: mouse chromosome name. Possible values are
names for the autosomal, sexual or mitochondrial chromosomes.