IGVsnap | R Documentation |
The function builds a script file that can be run on IGV to generate multiple screenshots at specific genomic regions.
IGVsnap(
loci_vector,
input_type,
biomart = "ensembl",
dataset = "mmusculus_gene_ensembl",
reference_genome = NULL,
fivePrime = 1000,
threePrime = 1000,
snap_names = NULL,
IGV_batch_file = paste(getwd(), "/IGV_batch.txt", sep = ""),
snap_image_format = "png",
snap_directory = getwd(),
maxPanelHeight = 1000,
delay.interval = 10,
session = NULL,
exit = FALSE
)
loci_vector |
Either a gene name vector (e.g. |
input_type |
Define the input type. Allowed values are |
biomart |
Defines the |
dataset |
Defines the |
reference_genome |
[optional] Defines the genome to use, e.g. "mm9", "mm10", "hg19", "hg38", ... . By default |
fivePrime |
Numeric value to define of how many base-pairs (bp) expand from full gene position at it's 5'-end, default 1000bp. |
threePrime |
Numeric value to define of how many base-pairs (bp) expand from full gene position at it's 3'-end, default 1000bp. |
snap_names |
[optional] String vector to define the names of images (without extention), by default uses |
IGV_batch_file |
String for the batch_script_file_name/path, by default |
snap_image_format |
String to define the format of the images, e.g. "png", "jpeg", "svg", ... . By default |
snap_directory |
String for the output directory for the snapshoots. By default <working_directory>. |
maxPanelHeight |
Numeric value to define the height in pixel of the IGV pannel that will be captured on IGV. By default |
delay.interval |
Sets a delay (sleep) time in milliseconds. The sleep interval is invoked between successive commands. By default |
session |
[optional] FULL path to an IGV session file (session.xml) to use for the images. By default |
exit |
Logical value to indicate whether exit IGV after image capture ended. By default |
To run the script on IGV: Tools > Run Batch Script... > choose the .txt output file from this function.
For more info on how batch tasks work on IGV see:
https://software.broadinstitute.org/software/igv/PortCommands.
Exports a .txt file ready-to-use on IGV.
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