align_matrices |
Align the rows and columns of two (or more) matrices |
annotate.gct |
Add annotations to a GCT object |
annotate_gct |
Add annotations to a GCT object |
annotate_gct-method |
Add annotations to a GCT object |
cdesc_char |
An example table of metadata, as would be parsed from or parse.gctx. Initially all the columns are of type character. |
check_colnames |
Check whether 'test_names' are columns in the 'data.frame' df |
check_dups |
Check for duplicates in a vector |
distil |
Collapse the rows or columns of a matrix using weighted averaging |
ds |
An example of a GCT object with row and column metadata and gene expression values in the matrix. |
extract.gct |
Exract elements from a GCT matrix |
extract_gct |
Exract elements from a GCT matrix |
GCT |
Initialize an object of class 'GCT' |
GCT-class |
An S4 class to represent a GCT object |
gene_set |
An example collection of gene sets as used in the Lamb 2006 CMap paper. |
ids |
Extract the or set row or column ids of a GCT object |
ids-method |
Extract the or set row or column ids of a GCT object |
ids<--method |
Extract the or set row or column ids of a GCT object |
is.wholenumber |
Check if x is a whole number |
kd_gct |
An example GCT object of knockdown experiments targeting a subset of landmark genes. |
lxb2mat |
Read an LXB file and return a matrix |
mat |
Extract or set the matrix of GCT object |
mat-method |
Extract or set the matrix of GCT object |
mat<--method |
Extract or set the matrix of GCT object |
melt.gct |
Transform a GCT object in to a long form 'data.table' (aka 'melt') |
melt_gct |
Transform a GCT object in to a long form 'data.table' (aka 'melt') |
melt_gct-method |
Transform a GCT object in to a long form 'data.table' (aka 'melt') |
merge.gct |
Merge two GCT objects together |
merge_gct |
Merge two GCT objects together |
merge_gct-method |
Merge two GCT objects together |
meta |
Extract the or set metadata of a GCT object |
meta-method |
Extract the or set metadata of a GCT object |
meta<--method |
Extract the or set metadata of a GCT object |
na_pad_matrix |
Pad a matrix with additional rows/columns of NA values |
parse.gctx |
Parse a GCTX file into the workspace as a GCT object |
parse.gmt |
Read a GMT file and return a list |
parse.gmx |
Read a GMX file and return a list |
parse.grp |
Read a GRP file and return a vector of its contents |
parse_gctx |
Parse a GCTX file into the workspace as a GCT object |
parse_gmt |
Read a GMT file and return a list |
parse_gmx |
Read a GMX file and return a list |
parse_grp |
Read a GRP file and return a vector of its contents |
rank.gct |
Convert a GCT object's matrix to ranks |
rank_gct |
Convert a GCT object's matrix to ranks |
rank_gct-method |
Convert a GCT object's matrix to ranks |
read.gctx.ids |
Read GCTX row or column ids |
read.gctx.meta |
Parse row or column metadata from GCTX files |
read_gctx_ids |
Read GCTX row or column ids |
read_gctx_meta |
Parse row or column metadata from GCTX files |
robust_zscore |
Compoute robust z-scores |
subset.gct |
Subset a gct object using the provided row and column ids |
subset_gct |
Subset a gct object using the provided row and column ids |
subset_gct-method |
Subset a gct object using the provided row and column ids |
threshold |
Threshold a numeric vector |
transpose.gct |
Transpose a GCT object |
transpose_gct |
Transpose a GCT object |
transpose_gct-method |
Transpose a GCT object |
update.gctx |
Update the matrix of an existing GCTX file |
update_gctx |
Update the matrix of an existing GCTX file |
write.gct |
Write a GCT object to disk in GCT format |
write.gctx |
Write a GCT object to disk in GCTX format |
write.tbl |
Write a 'data.frame' to a tab-delimited text file |
write_gct |
Write a GCT object to disk in GCT format |
write_gctx |
Write a GCT object to disk in GCTX format |
write_gmt |
Write a nested list to a GMT file |
write_grp |
Write a vector to a GRP file |
write_tbl |
Write a 'data.frame' to a tab-delimited text file |