readISS: Read ISS data

In mashranga/MolDia: Single cell In-Situ sequencing (ISS) data analysis

Description

Read ISS data

Usage

readISS(file, segment = TRUE, cellid = "CellID", centX = NULL,
  centY = NULL, genepos = NULL, geneposOPT = "OR", rpc = 1,
  rpg = 1, gene = NULL, nogene = NULL)

Arguments

file	File name in CSV format.Also data formate in "data.frame" class and "MolDiaISS"(Segment) & 'MolDiaISS_nonsegment'(Non-segment) class (Output of readISS).
segment	If the file is segmentated or not. TRUE/FALSE needed. Default if TRUE. See details for file structure,
cellid	String to naming cell. Default is "CellID".
centX	Name of X co-ordinate in file. Default is "centroidX"
centY	Name of Y co-ordinate in file Default is "centroidY"
genepos	Name of genes to consider for gene positive cells. Default is NULL
geneposOPT	Only work when 'genepos' has a value. "AND", "OR" and "NONE" condition for genepos. Default is "OR".
rpc	Total reads per cell to be consider. Default is 1.
rpg	Total reads per gene to be consider. Default is 1.
gene	Gene names to be consider. Object in vector or list class. In list formated input, every list element is a group of interested genes. Every list element should have a name. Default is NULL.
nogene	Gene name to exclude from data. Default is NULL.

Details

File structure of non-segmentated input:

For non-segmentated file input, there should be 9 column. 7 column names are "Read", "Gene", "ParentCell", "Tile", "MinAnchor", "MinQuality" and "MinAlign". Rest 2 column are x and y axix position and defined by 'centX' and 'centY' parameter.

Value

Output will be a object in class MolDiaISS or MolDiaISS_nonsegment. See detail MolDiaISS and MolDiaISS_nonsegment

Author(s)

Mohammad Tanvir Ahamed

Examples

##### Reading ISS data from CSV formate
data_1 <- readISS(file = system.file("extdata", "CellBlobs_QT_0.35.csv", package="MolDia"),
                  cellid = "CellID", centX = "centroidX", centY = "centroidY")
data_2 <- readISS(file = system.file("extdata", "CellBlobs_QT_0.40.csv", package="MolDia"),
                  cellid = "CellID",centX = "centroidX", centY = "centroidY")
data_3 <- readISS(file = system.file("extdMinQualityata", "Hypocampus_left.csv", package="MolDia"),
                  cellid = "CellId",centX = "centroid_x", centY = "centroid_y")
data_4 <- readISS(file = system.file("extdata", "Hypocampus_right.csv", package="MolDia"),
                  cellid = "CellId",centX = "centroid_x", centY = "centroid_y")

###### Merge genes of interest into groups and plot
data(marker_gene)
data_5 <- readISS(file = data_4, gene = marker_gene)
result <- ISS_map(data = data_5, what = "cell", gene = data_5@gene[1:8]) 


## Not RUN
## Read RCA data in dataframe formate
#gene <- data_3@gene[1:3]
#data(single_cell)
#single_cell$CellID <- rownames(single_cell)
#Note: Big data. Take long time to load without selected gene
#data_sc <- readISS(file = single_cell, cellid = "CellID",gene= gene) 

###### Reading non-segmentated file
data_6 <- readISS(file = system.file("extdata", "nonSeg_QT_0.35_0_details.csv", package="MolDia"), segment = FALSE,
                  centX = "PosX", centY = "PosY", nogene = "NNNN")
data_7 <- readISS(file = data_6, gene= c("Gdf7","WNT1","Pak3","Tfap2a"))
data_8 <- readISS(file = data_7, nogene = c("Gdf7","WNT1"))

mashranga/MolDia documentation built on May 26, 2019, 9:36 a.m.