NEWS.md

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

QCnormSE 0.99.4.9000

bug fixes

check_sex() - set k to odd number <= minimal group size

combine_se_objects() - check if column names are unique

extract_scan_date() - use correct sample file

plot_mds_pca() - use C for column names in MDS plot - percentage of variance explained only for PCA

modifications

combine_se_objects() - add option to merge meta data - make function more flexible (e.g. no overlapping columns in colData possible, select common assays)

plot_distribution() - add option to specify axis label

QCnormSE 0.99.4

modifications

remove_genes() - additional arguments in edgeR method

bug fix

remove_genes() - correct passing of freq argument in edgeR method

QCnormSE 0.99.3

modifications

remove_samples() - if freq = 1 remove all samples for which criterion is fullfilled for all genes

detect_duplicated_samples() - add parameters to optionally remove genes with missing values and to specify method to deal with missing values in cor and covar functions

QCnormSE 0.99.2

bug fixes

combine_se_objects() - set metadata of combined SE object to empty list

extract_scan_date() - create temp.dir if it does not exist

get_outliers_mds_pca_2d() (internal function) - convert from list to vector if duplicate values occur in outlier detection

plot_heatmap() - include lower limits of intervals when defining color categories of P-values

remove_genes() - if freq = 1 remove all genes for which criterion is fullfilled for all samples

modifications

aggregate_by_new_id() - keep all assays - remove method "sum" since not all assays can be kept if expression values of several probes are summed up

QCnormSE 0.99.1

bug fixes

check_sex() - sex.column can now also be a factor - error if none of the genes in se overlap with genes in info.sex.genes

define_batches() - ensure that scan.date is of class Date

extract_scan_date() - col.sample.id can now also be a factor - additional possible date format for CEL files - different positions of scan date information possible in Agilent raw files

detect_duplicate_samples() - more than one duplicate shown as vertical red line

plot_mds_pca_2d() - remove unused levels of var.color and var.shape

new features

new function combine_se_objects()

modifications

check_batch_effects() - additional heatmap showing absolute adjusted r^2 values

check_sex() - rownames can be used as gene identifier - add ellipses to MDS plot

detect_duplicate_samples() - improve performance by using default values of function stats::cor() and provide access to fast implementation in R package coop - add option to set title of plot

extract_scan_date() add option to specify column with sample information

QCnormSE 0.99.0

• initial commit

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.